diff --git a/src/management/instance-directory.ts b/src/management/instance-directory.ts
index ab5a15c9..82ca0e96 100644
--- a/src/management/instance-directory.ts
+++ b/src/management/instance-directory.ts
@@ -15,7 +15,7 @@ function unsafeInstancePath(targetPath: string): never {
   });
 }
 
-interface DirectoryIdentity {
+export interface DirectoryIdentity {
   device: number;
   inode: number;
   realPath: string;
@@ -115,6 +115,39 @@ export function assertSafeAccountInstancePath(instancesDir: string, instancePath
   if (!isSafeAccountInstancePath(instancesDir, instancePath)) unsafeInstancePath(instancePath);
 }
 
+/**
+ * Capture the validated directory identity used by later mutation guards.
+ * This is defense-in-depth for static and ordinary concurrent replacement,
+ * not a hostile same-UID race boundary; that would require dirfd/openat-style APIs.
+ */
+export function captureSafeAccountInstanceIdentity(
+  instancesDir: string,
+  instancePath: string
+): DirectoryIdentity {
+  assertSafeAccountInstancePath(instancesDir, instancePath);
+  const identity = readDirectoryIdentity(instancePath);
+  assertAccountInstanceIdentity(instancesDir, instancePath, identity);
+  return identity;
+}
+
+/** Require the lexical instance path to still name the validated directory. */
+export function assertAccountInstanceIdentity(
+  instancesDir: string,
+  instancePath: string,
+  expectedIdentity: DirectoryIdentity
+): void {
+  if (!isSafeAccountInstancePath(instancesDir, instancePath)) unsafeInstancePath(instancePath);
+
+  let currentIdentity: DirectoryIdentity;
+  try {
+    currentIdentity = readDirectoryIdentity(instancePath);
+  } catch {
+    unsafeInstancePath(instancePath);
+  }
+
+  if (!identitiesMatch(expectedIdentity, currentIdentity)) unsafeInstancePath(instancePath);
+}
+
 export function listAccountInstanceNames(instancesDir: string): string[] {
   if (!fs.existsSync(instancesDir)) {
     return [];
diff --git a/src/management/shared-manager/plugin-layout-internals.ts b/src/management/shared-manager/plugin-layout-internals.ts
index 0c9c2cf0..c215536b 100644
--- a/src/management/shared-manager/plugin-layout-internals.ts
+++ b/src/management/shared-manager/plugin-layout-internals.ts
@@ -39,6 +39,18 @@ import type { SharedItem } from './types';
  */
 export type PluginLayoutRoots = PluginMetadataRoots;
 
+function runGuardedInstanceMutation<T>(
+  assertInstanceIdentity: (() => void) | undefined,
+  operation: () => T
+): T {
+  assertInstanceIdentity?.();
+  try {
+    return operation();
+  } finally {
+    assertInstanceIdentity?.();
+  }
+}
+
 /**
  * Ensure the plugin layout default directories (cache, marketplaces) and
  * registry files (installed_plugins.json, known_marketplaces.json) exist
@@ -75,7 +87,11 @@ export function ensureSharedPluginLayoutDefaults(claudeDir: string): void {
  * Link shared plugins directory entries into an instance, creating the
  * instance plugins directory first if needed.
  */
-export function linkInstancePlugins(roots: PluginLayoutRoots, instancePath: string): void {
+export function linkInstancePlugins(
+  roots: PluginLayoutRoots,
+  instancePath: string,
+  assertInstanceIdentity?: () => void
+): void {
   const linkPath = path.join(instancePath, 'plugins');
   const targetPath = path.join(roots.sharedDir, 'plugins');
   let linkStats: fs.Stats | null = null;
@@ -87,30 +103,42 @@ export function linkInstancePlugins(roots: PluginLayoutRoots, instancePath: stri
       throw err;
     }
   }
+  assertInstanceIdentity?.();
 
   if (linkStats?.isSymbolicLink() || (linkStats && !linkStats.isDirectory())) {
-    removeExistingPath(linkPath, linkStats.isDirectory() ? 'directory' : 'file');
+    const existingType = linkStats.isDirectory() ? 'directory' : 'file';
+    runGuardedInstanceMutation(assertInstanceIdentity, () =>
+      removeExistingPath(linkPath, existingType)
+    );
   }
 
   if (!linkStats || !linkStats.isDirectory()) {
-    fs.mkdirSync(linkPath, { recursive: true, mode: 0o700 });
+    runGuardedInstanceMutation(assertInstanceIdentity, () =>
+      fs.mkdirSync(linkPath, { recursive: true, mode: 0o700 })
+    );
   }
 
-  for (const item of getSharedPluginLinkItems(roots.sharedDir)) {
+  const linkItems = getSharedPluginLinkItems(roots.sharedDir);
+  assertInstanceIdentity?.();
+
+  for (const item of linkItems) {
     const targetEntryPath = path.join(targetPath, item.name);
     const linkEntryPath = path.join(linkPath, item.name);
     let adoption: ReturnType<typeof adoptDivergedFileContent> = 'not-claimed';
 
     if (item.type === 'file') {
-      adoption = adoptDivergedFileContent(
-        linkEntryPath,
-        path.join(roots.claudeDir, 'plugins', item.name)
+      adoption = runGuardedInstanceMutation(assertInstanceIdentity, () =>
+        adoptDivergedFileContent(linkEntryPath, path.join(roots.claudeDir, 'plugins', item.name))
       );
       if (adoption === 'not-claimed') {
-        removeExistingPath(linkEntryPath, item.type);
+        runGuardedInstanceMutation(assertInstanceIdentity, () =>
+          removeExistingPath(linkEntryPath, item.type)
+        );
       }
     } else {
-      removeExistingPath(linkEntryPath, item.type);
+      runGuardedInstanceMutation(assertInstanceIdentity, () =>
+        removeExistingPath(linkEntryPath, item.type)
+      );
     }
     assertAdoptionPathAbsent(linkEntryPath, adoption);
 
@@ -119,10 +147,12 @@ export function linkInstancePlugins(roots: PluginLayoutRoots, instancePath: stri
       continue;
     }
 
+    assertInstanceIdentity?.();
     try {
       const symlinkType = item.type === 'directory' ? 'dir' : 'file';
       fs.symlinkSync(targetEntryPath, linkEntryPath, symlinkType);
     } catch (_err) {
+      assertInstanceIdentity?.();
       assertAdoptionPathAbsent(linkEntryPath, adoption);
       if (getLstatSync(linkEntryPath)) {
         console.log(warn(`Skipping plugins/${item.name}: path reappeared during reconciliation`));
@@ -130,9 +160,13 @@ export function linkInstancePlugins(roots: PluginLayoutRoots, instancePath: stri
       }
       if (process.platform === 'win32') {
         if (item.type === 'directory') {
-          copyDirectoryFallback(targetEntryPath, linkEntryPath);
+          runGuardedInstanceMutation(assertInstanceIdentity, () =>
+            copyDirectoryFallback(targetEntryPath, linkEntryPath)
+          );
         } else {
-          fs.copyFileSync(targetEntryPath, linkEntryPath, fs.constants.COPYFILE_EXCL);
+          runGuardedInstanceMutation(assertInstanceIdentity, () =>
+            fs.copyFileSync(targetEntryPath, linkEntryPath, fs.constants.COPYFILE_EXCL)
+          );
         }
         console.log(
           warn(`Symlink failed for plugins/${item.name}, copied instead (enable Developer Mode)`)
@@ -141,6 +175,7 @@ export function linkInstancePlugins(roots: PluginLayoutRoots, instancePath: stri
         throw _err;
       }
     }
+    assertInstanceIdentity?.();
   }
 }
 
diff --git a/src/management/shared-manager/shared-dir-linker.ts b/src/management/shared-manager/shared-dir-linker.ts
index 94072f05..b339f619 100644
--- a/src/management/shared-manager/shared-dir-linker.ts
+++ b/src/management/shared-manager/shared-dir-linker.ts
@@ -18,7 +18,10 @@ import * as fs from 'fs';
 import * as path from 'path';
 
 import { info, warn } from '../../utils/ui';
-import { isSafeAccountInstancePath } from '../instance-directory';
+import {
+  assertAccountInstanceIdentity,
+  captureSafeAccountInstanceIdentity,
+} from '../instance-directory';
 import {
   adoptDivergedFileContent,
   assertAdoptionPathAbsent,
@@ -54,6 +57,18 @@ import { SHARED_ITEMS } from './types';
  */
 export type LinkerRoots = PluginMetadataRoots;
 
+function runInstanceMutationStage<T>(
+  assertInstanceIdentity: (() => void) | undefined,
+  operation: () => T
+): T {
+  assertInstanceIdentity?.();
+  try {
+    return operation();
+  } finally {
+    assertInstanceIdentity?.();
+  }
+}
+
 /**
  * Detect a circular symlink before creation. A symlink is circular when its
  * target (raw or canonical) points back inside the shared root.
@@ -102,104 +117,115 @@ export function detectCircularSymlink(target: string, sharedDir: string): boolea
  * Ensure shared directories exist as symlinks to ~/.claude/ and that the
  * plugin layout default directories and registry files are present.
  */
-export function ensureSharedDirectories(roots: LinkerRoots): void {
+export function ensureSharedDirectories(
+  roots: LinkerRoots,
+  assertInstanceIdentity?: () => void
+): void {
   const claudeDir = roots.claudeDir;
   const sharedDir = roots.sharedDir;
 
-  if (!getLstatSync(claudeDir)) {
-    console.log(info('Creating ~/.claude/ directory structure'));
-    fs.mkdirSync(claudeDir, { recursive: true, mode: 0o700 });
-  }
+  runInstanceMutationStage(assertInstanceIdentity, () => {
+    if (!getLstatSync(claudeDir)) {
+      console.log(info('Creating ~/.claude/ directory structure'));
+      fs.mkdirSync(claudeDir, { recursive: true, mode: 0o700 });
+    }
+  });
 
-  if (!getLstatSync(sharedDir)) {
-    fs.mkdirSync(sharedDir, { recursive: true, mode: 0o700 });
-  }
+  runInstanceMutationStage(assertInstanceIdentity, () => {
+    if (!getLstatSync(sharedDir)) {
+      fs.mkdirSync(sharedDir, { recursive: true, mode: 0o700 });
+    }
+  });
 
-  ensureSharedPluginLayoutDefaults(claudeDir);
+  runInstanceMutationStage(assertInstanceIdentity, () =>
+    ensureSharedPluginLayoutDefaults(claudeDir)
+  );
 
   for (const item of SHARED_ITEMS) {
-    const claudePath = path.join(claudeDir, item.name);
-    const sharedPath = path.join(sharedDir, item.name);
+    runInstanceMutationStage(assertInstanceIdentity, () => {
+      const claudePath = path.join(claudeDir, item.name);
+      const sharedPath = path.join(sharedDir, item.name);
 
-    if (item.type === 'file') {
-      recoverOrphanedCanonicalClaim(claudePath);
-    }
-
-    if (item.type === 'file' && item.divergencePolicy === 'canonical-first') {
-      reconcileCanonicalFirstFile(roots, item.name);
-    }
-
-    if (!getLstatSync(claudePath)) {
-      if (item.type === 'directory') {
-        fs.mkdirSync(claudePath, { recursive: true, mode: 0o700 });
-      } else if (item.type === 'file') {
-        fs.writeFileSync(claudePath, item.seedContent, 'utf8');
-      }
-    }
-
-    if (detectCircularSymlink(claudePath, sharedDir)) {
-      console.log(warn(`Skipping ${item.name}: circular symlink detected`));
-      continue;
-    }
-
-    let sharedAdoption: ReturnType<typeof adoptDivergedFileContent> = 'not-claimed';
-    if (getLstatSync(sharedPath)) {
-      let removeExisting = true;
-      try {
-        const stats = fs.lstatSync(sharedPath);
-        if (stats.isSymbolicLink()) {
-          const currentTarget = fs.readlinkSync(sharedPath);
-          const resolvedTarget = path.resolve(path.dirname(sharedPath), currentTarget);
-          if (resolvedTarget === claudePath) {
-            continue;
-          }
-        }
-      } catch (_err) {
-        // Continue to recreate
+      if (item.type === 'file') {
+        recoverOrphanedCanonicalClaim(claudePath);
       }
 
       if (item.type === 'file' && item.divergencePolicy === 'canonical-first') {
-        removeExisting = !preserveCanonicalFirstDivergence(sharedPath, claudePath);
-      } else if (item.type === 'file') {
-        sharedAdoption = adoptDivergedFileContent(sharedPath, claudePath);
-        removeExisting = sharedAdoption === 'not-claimed';
+        reconcileCanonicalFirstFile(roots, item.name);
       }
 
-      if (item.type === 'directory' && removeExisting) {
-        fs.rmSync(sharedPath, { recursive: true, force: true });
-      } else if (removeExisting) {
-        fs.unlinkSync(sharedPath);
+      if (!getLstatSync(claudePath)) {
+        if (item.type === 'directory') {
+          fs.mkdirSync(claudePath, { recursive: true, mode: 0o700 });
+        } else if (item.type === 'file') {
+          fs.writeFileSync(claudePath, item.seedContent, 'utf8');
+        }
       }
-      assertAdoptionPathAbsent(sharedPath, sharedAdoption);
-    }
 
-    if (getLstatSync(sharedPath)) {
-      console.log(warn(`Skipping ${item.name}: path reappeared during reconciliation`));
-      continue;
-    }
+      if (detectCircularSymlink(claudePath, sharedDir)) {
+        console.log(warn(`Skipping ${item.name}: circular symlink detected`));
+        return;
+      }
+
+      let sharedAdoption: ReturnType<typeof adoptDivergedFileContent> = 'not-claimed';
+      if (getLstatSync(sharedPath)) {
+        let removeExisting = true;
+        try {
+          const stats = fs.lstatSync(sharedPath);
+          if (stats.isSymbolicLink()) {
+            const currentTarget = fs.readlinkSync(sharedPath);
+            const resolvedTarget = path.resolve(path.dirname(sharedPath), currentTarget);
+            if (resolvedTarget === claudePath) {
+              return;
+            }
+          }
+        } catch (_err) {
+          // Continue to recreate
+        }
+
+        if (item.type === 'file' && item.divergencePolicy === 'canonical-first') {
+          removeExisting = !preserveCanonicalFirstDivergence(sharedPath, claudePath);
+        } else if (item.type === 'file') {
+          sharedAdoption = adoptDivergedFileContent(sharedPath, claudePath);
+          removeExisting = sharedAdoption === 'not-claimed';
+        }
+
+        if (item.type === 'directory' && removeExisting) {
+          fs.rmSync(sharedPath, { recursive: true, force: true });
+        } else if (removeExisting) {
+          fs.unlinkSync(sharedPath);
+        }
+        assertAdoptionPathAbsent(sharedPath, sharedAdoption);
+      }
 
-    try {
-      const symlinkType = item.type === 'directory' ? 'dir' : 'file';
-      fs.symlinkSync(claudePath, sharedPath, symlinkType);
-    } catch (_err) {
-      assertAdoptionPathAbsent(sharedPath, sharedAdoption);
       if (getLstatSync(sharedPath)) {
         console.log(warn(`Skipping ${item.name}: path reappeared during reconciliation`));
-        continue;
+        return;
       }
-      if (process.platform === 'win32') {
-        if (item.type === 'directory') {
-          copyDirectoryFallback(claudePath, sharedPath);
-        } else if (item.type === 'file') {
-          fs.copyFileSync(claudePath, sharedPath, fs.constants.COPYFILE_EXCL);
+
+      try {
+        const symlinkType = item.type === 'directory' ? 'dir' : 'file';
+        fs.symlinkSync(claudePath, sharedPath, symlinkType);
+      } catch (_err) {
+        assertAdoptionPathAbsent(sharedPath, sharedAdoption);
+        if (getLstatSync(sharedPath)) {
+          console.log(warn(`Skipping ${item.name}: path reappeared during reconciliation`));
+          return;
+        }
+        if (process.platform === 'win32') {
+          if (item.type === 'directory') {
+            copyDirectoryFallback(claudePath, sharedPath);
+          } else if (item.type === 'file') {
+            fs.copyFileSync(claudePath, sharedPath, fs.constants.COPYFILE_EXCL);
+          }
+          console.log(
+            warn(`Symlink failed for ${item.name}, copied instead (enable Developer Mode)`)
+          );
+        } else {
+          throw _err;
         }
-        console.log(
-          warn(`Symlink failed for ${item.name}, copied instead (enable Developer Mode)`)
-        );
-      } else {
-        throw _err;
       }
-    }
+    });
   }
 }
 
@@ -207,73 +233,79 @@ export function ensureSharedDirectories(roots: LinkerRoots): void {
  * Link shared directories into a specific instance path.
  */
 export function linkSharedDirectories(roots: LinkerRoots, instancePath: string): void {
-  if (!isSafeAccountInstancePath(roots.instancesDir, instancePath)) {
-    throw Object.assign(new TypeError(`Unsafe account instance path: ${instancePath}`), {
-      code: 'EINVAL',
-    });
-  }
-  ensureSharedDirectories(roots);
+  const instanceIdentity = captureSafeAccountInstanceIdentity(roots.instancesDir, instancePath);
+  const assertInstanceIdentity = () =>
+    assertAccountInstanceIdentity(roots.instancesDir, instancePath, instanceIdentity);
+
+  ensureSharedDirectories(roots, assertInstanceIdentity);
+  assertInstanceIdentity();
 
   const sharedDir = roots.sharedDir;
 
   for (const item of SHARED_ITEMS) {
-    if (item.name === 'plugins') {
-      linkInstancePlugins(roots, instancePath);
-      continue;
-    }
+    runInstanceMutationStage(assertInstanceIdentity, () => {
+      if (item.name === 'plugins') {
+        linkInstancePlugins(roots, instancePath, assertInstanceIdentity);
+        return;
+      }
 
-    const linkPath = path.join(instancePath, item.name);
-    const targetPath = path.join(sharedDir, item.name);
-    let adoption: ReturnType<typeof adoptDivergedFileContent> = 'not-claimed';
+      const linkPath = path.join(instancePath, item.name);
+      const targetPath = path.join(sharedDir, item.name);
+      let adoption: ReturnType<typeof adoptDivergedFileContent> = 'not-claimed';
 
-    if (item.type === 'file' && item.divergencePolicy === 'canonical-first') {
-      if (!preserveCanonicalFirstDivergence(linkPath, path.join(roots.claudeDir, item.name))) {
+      if (item.type === 'file' && item.divergencePolicy === 'canonical-first') {
+        if (!preserveCanonicalFirstDivergence(linkPath, path.join(roots.claudeDir, item.name))) {
+          removeExistingPath(linkPath, item.type);
+        }
+      } else if (item.type === 'file') {
+        adoption = adoptDivergedFileContent(linkPath, path.join(roots.claudeDir, item.name));
+        if (adoption === 'not-claimed') {
+          removeExistingPath(linkPath, item.type);
+        }
+      } else {
         removeExistingPath(linkPath, item.type);
       }
-    } else if (item.type === 'file') {
-      adoption = adoptDivergedFileContent(linkPath, path.join(roots.claudeDir, item.name));
-      if (adoption === 'not-claimed') {
-        removeExistingPath(linkPath, item.type);
-      }
-    } else {
-      removeExistingPath(linkPath, item.type);
-    }
-    assertAdoptionPathAbsent(linkPath, adoption);
-
-    if (getLstatSync(linkPath)) {
-      console.log(warn(`Skipping ${item.name}: path reappeared during reconciliation`));
-      continue;
-    }
-
-    try {
-      const symlinkType = item.type === 'directory' ? 'dir' : 'file';
-      fs.symlinkSync(targetPath, linkPath, symlinkType);
-    } catch (_err) {
       assertAdoptionPathAbsent(linkPath, adoption);
+
       if (getLstatSync(linkPath)) {
         console.log(warn(`Skipping ${item.name}: path reappeared during reconciliation`));
-        continue;
+        return;
       }
-      if (process.platform === 'win32') {
-        if (item.type === 'directory') {
-          copyDirectoryFallback(targetPath, linkPath);
-        } else if (item.type === 'file') {
-          fs.copyFileSync(targetPath, linkPath, fs.constants.COPYFILE_EXCL);
+
+      try {
+        const symlinkType = item.type === 'directory' ? 'dir' : 'file';
+        fs.symlinkSync(targetPath, linkPath, symlinkType);
+      } catch (_err) {
+        assertAdoptionPathAbsent(linkPath, adoption);
+        if (getLstatSync(linkPath)) {
+          console.log(warn(`Skipping ${item.name}: path reappeared during reconciliation`));
+          return;
+        }
+        if (process.platform === 'win32') {
+          if (item.type === 'directory') {
+            copyDirectoryFallback(targetPath, linkPath);
+          } else if (item.type === 'file') {
+            fs.copyFileSync(targetPath, linkPath, fs.constants.COPYFILE_EXCL);
+          }
+          console.log(
+            warn(`Symlink failed for ${item.name}, copied instead (enable Developer Mode)`)
+          );
+        } else {
+          throw _err;
         }
-        console.log(
-          warn(`Symlink failed for ${item.name}, copied instead (enable Developer Mode)`)
-        );
-      } else {
-        throw _err;
       }
-    }
+    });
   }
 
   // Preserve original behavior: linkSharedDirectories always concludes by
   // normalizing plugin + marketplace metadata for the freshly linked
   // instance. migrateFromV311 relies on this side effect.
-  normalizePluginRegistryPaths(roots, instancePath);
-  normalizeMarketplaceRegistryPaths(roots, instancePath);
+  runInstanceMutationStage(assertInstanceIdentity, () =>
+    normalizePluginRegistryPaths(roots, instancePath)
+  );
+  runInstanceMutationStage(assertInstanceIdentity, () =>
+    normalizeMarketplaceRegistryPaths(roots, instancePath)
+  );
 }
 
 /**
diff --git a/tests/unit/shared-claude-memory.test.ts b/tests/unit/shared-claude-memory.test.ts
index 4bfb4e09..9ec355e0 100644
--- a/tests/unit/shared-claude-memory.test.ts
+++ b/tests/unit/shared-claude-memory.test.ts
@@ -62,6 +62,18 @@ describe('shared CLAUDE.md memory', () => {
     expect(path.resolve(path.dirname(filePath), fs.readlinkSync(filePath))).toBe(targetPath);
   }
 
+  function expectInvalidInstancePath(operation: () => void): void {
+    let thrown: unknown;
+    try {
+      operation();
+    } catch (error) {
+      thrown = error;
+    }
+
+    expect(thrown).toBeInstanceOf(TypeError);
+    expect((thrown as NodeJS.ErrnoException).code).toBe('EINVAL');
+  }
+
   beforeEach(() => {
     tempHome = fs.mkdtempSync(path.join(os.tmpdir(), 'ccs-shared-claude-memory-'));
     originalHome = process.env.HOME;
@@ -326,6 +338,98 @@ describe('shared CLAUDE.md memory', () => {
     expect(fs.readFileSync(conflictFiles(instanceFile('work'))[0], 'utf8')).toBe('# Claimed\n');
   });
 
+  it('aborts when the instance root is replaced during shared-root setup', () => {
+    const manager = new SharedManager();
+    const workInstance = instanceDir('work');
+    const originalInstance = instanceDir('work-original');
+    const externalInstance = path.join(tempHome, 'external-work');
+    const sentinelPath = path.join(externalInstance, 'sentinel.bin');
+    const sentinel = Buffer.from([0x00, 0x7f, 0x80, 0xff]);
+    fs.mkdirSync(workInstance, { recursive: true });
+    fs.mkdirSync(externalInstance, { recursive: true });
+    fs.mkdirSync(path.join(tempHome, '.claude'), { recursive: true });
+    fs.mkdirSync(path.join(ccsDir(), 'shared'), { recursive: true });
+    fs.writeFileSync(sentinelPath, sentinel);
+
+    const originalMkdirSync = fs.mkdirSync;
+    let replaced = false;
+    spyOn(fs, 'mkdirSync').mockImplementation(((targetPath, options) => {
+      if (!replaced && String(targetPath) === path.join(tempHome, '.claude', 'plugins')) {
+        replaced = true;
+        fs.renameSync(workInstance, originalInstance);
+        fs.symlinkSync(externalInstance, workInstance, 'dir');
+      }
+      return originalMkdirSync(targetPath, options);
+    }) as typeof fs.mkdirSync);
+
+    expectInvalidInstancePath(() => manager.linkSharedDirectories(workInstance));
+    expect(fs.readFileSync(sentinelPath)).toEqual(sentinel);
+    expect(fs.readdirSync(externalInstance)).toEqual(['sentinel.bin']);
+  });
+
+  it('does not reconcile a regular replacement directory during shared-root setup', () => {
+    const manager = new SharedManager();
+    const workInstance = instanceDir('work');
+    const originalInstance = instanceDir('work-original');
+    const replacementFixture = path.join(tempHome, 'replacement-work');
+    const replacementMemory = path.join(replacementFixture, 'CLAUDE.md');
+    const sentinelPath = path.join(replacementFixture, 'sentinel.bin');
+    const memoryBytes = Buffer.from([0x23, 0x20, 0x80, 0xff, 0x0a]);
+    const sentinel = Buffer.from([0x11, 0x22, 0x33, 0x44]);
+    fs.mkdirSync(workInstance, { recursive: true });
+    fs.mkdirSync(replacementFixture, { recursive: true });
+    fs.mkdirSync(path.join(tempHome, '.claude'), { recursive: true });
+    fs.mkdirSync(path.join(ccsDir(), 'shared'), { recursive: true });
+    fs.writeFileSync(replacementMemory, memoryBytes);
+    fs.writeFileSync(sentinelPath, sentinel);
+
+    const originalMkdirSync = fs.mkdirSync;
+    let replaced = false;
+    spyOn(fs, 'mkdirSync').mockImplementation(((targetPath, options) => {
+      if (!replaced && String(targetPath) === path.join(tempHome, '.claude', 'plugins')) {
+        replaced = true;
+        fs.renameSync(workInstance, originalInstance);
+        fs.renameSync(replacementFixture, workInstance);
+      }
+      return originalMkdirSync(targetPath, options);
+    }) as typeof fs.mkdirSync);
+
+    expectInvalidInstancePath(() => manager.linkSharedDirectories(workInstance));
+    expect(fs.readFileSync(path.join(workInstance, 'CLAUDE.md'))).toEqual(memoryBytes);
+    expect(fs.readFileSync(path.join(workInstance, 'sentinel.bin'))).toEqual(sentinel);
+    expect(fs.readdirSync(workInstance).sort()).toEqual(['CLAUDE.md', 'sentinel.bin']);
+  });
+
+  it('aborts when the instance root is replaced during plugin linking', () => {
+    const manager = new SharedManager();
+    const workInstance = instanceDir('work');
+    const originalInstance = instanceDir('work-original');
+    const externalInstance = path.join(tempHome, 'external-work');
+    const externalPlugins = path.join(externalInstance, 'plugins');
+    const sentinelPath = path.join(externalPlugins, 'sentinel.bin');
+    const sentinel = Buffer.from([0x10, 0x20, 0x30, 0x40]);
+    fs.mkdirSync(path.join(workInstance, 'plugins'), { recursive: true });
+    fs.mkdirSync(externalPlugins, { recursive: true });
+    fs.writeFileSync(sentinelPath, sentinel);
+
+    const originalLstatSync = fs.lstatSync;
+    let replaced = false;
+    spyOn(fs, 'lstatSync').mockImplementation(((targetPath, options) => {
+      const result = originalLstatSync(targetPath, options);
+      if (!replaced && String(targetPath) === path.join(workInstance, 'plugins')) {
+        replaced = true;
+        fs.renameSync(workInstance, originalInstance);
+        fs.symlinkSync(externalInstance, workInstance, 'dir');
+      }
+      return result;
+    }) as typeof fs.lstatSync);
+
+    expectInvalidInstancePath(() => manager.linkSharedDirectories(workInstance));
+    expect(fs.readFileSync(sentinelPath)).toEqual(sentinel);
+    expect(fs.readdirSync(externalPlugins)).toEqual(['sentinel.bin']);
+    expect(fs.readdirSync(externalInstance)).toEqual(['plugins']);
+  });
+
   it('rejects linking through a symlinked instances root without touching its target', () => {
     const manager = new SharedManager();
     const managedInstances = path.join(ccsDir(), 'instances');