diff --git a/src/serena/config/serena_config.py b/src/serena/config/serena_config.py
index 4ba5c473..5ff9b8c4 100644
--- a/src/serena/config/serena_config.py
+++ b/src/serena/config/serena_config.py
@@ -958,6 +958,8 @@ class SerenaConfig(SharedConfig, ModeSelectionDefinitionWithBaseModes):
     the path to the configuration file to which updates of the configuration shall be saved;
     if None, the configuration is not saved to disk
     """
+    _projects_at_load: set[str] = field(default_factory=set, repr=False)
+    """Project roots present when this configuration instance was last persisted."""
 
     # *** static members ***
 
@@ -1096,6 +1098,8 @@ class SerenaConfig(SharedConfig, ModeSelectionDefinitionWithBaseModes):
             )
             instance.projects.append(project)
 
+        instance._projects_at_load = {str(project.project_root) for project in instance.projects}
+
         # determine language backend
         language_backend = get_dataclass_default(SerenaConfig, "language_backend")
         if "language_backend" in loaded_commented_yaml:
@@ -1295,22 +1299,38 @@ class SerenaConfig(SharedConfig, ModeSelectionDefinitionWithBaseModes):
         self._persist_projects()
 
     def _persist_projects(self) -> None:
-        """
-        Persists the list of registered projects, merging it with the list currently found on disk
-        (parallel agent instances may have added or removed projects in the meantime).
+        """Persist this instance's project-list changes without undoing concurrent edits.
+
+        The disk copy is reloaded because multiple agent processes may update the global
+        configuration concurrently. The instance baseline lets us distinguish this instance's
+        removals and additions from changes made by another process: unchanged baseline projects
+        follow the current disk copy, while removed baseline projects are filtered out and newly
+        added instance projects are appended.
         """
         if self.config_file_path is None:
             return
+
         persisted = SerenaConfig.from_config_file()
+        current_projects_by_path = {str(project.project_root): project for project in self.projects}
+        current_paths = set(current_projects_by_path)
+        removed_paths = self._projects_at_load - current_paths
+        added_paths = current_paths - self._projects_at_load
+
         combined_projects = []
         handled_project_paths = set()
-        for p in persisted.projects + self.projects:
-            str_path = str(p.project_root)
-            if str_path not in handled_project_paths:
-                combined_projects.append(p)
-                handled_project_paths.add(str_path)
+        for project in persisted.projects:
+            project_path = str(project.project_root)
+            if project_path not in removed_paths:
+                combined_projects.append(project)
+                handled_project_paths.add(project_path)
+        for project_path in added_paths:
+            if project_path not in handled_project_paths:
+                combined_projects.append(current_projects_by_path[project_path])
+                handled_project_paths.add(project_path)
+
         persisted.projects = combined_projects
         persisted._save()
+        self._projects_at_load = current_paths
 
     def _save(self) -> None:
         """
diff --git a/test/serena/config/test_serena_config.py b/test/serena/config/test_serena_config.py
index cc04ab45..529667f7 100644
--- a/test/serena/config/test_serena_config.py
+++ b/test/serena/config/test_serena_config.py
@@ -604,6 +604,48 @@ class TestSerenaConfigLoadSave:
 
         assert len(resulting_config.projects) == 4
 
+    def test_remove_project_persists_across_reload(self):
+        """Removing a project must update the on-disk project registry."""
+        p1 = self._make_project_dir("project1", 'project_name: "project1"\nlanguages: ["python"]\n')
+        p2 = self._make_project_dir("project2", 'project_name: "project2"\nlanguages: ["python"]\n')
+        self._write_master_config([p1, p2])
+
+        config = SerenaConfig.from_config_file(generate_if_missing=False)
+        config.remove_project("project2")
+
+        reloaded = SerenaConfig.from_config_file(generate_if_missing=False)
+        assert [project.project_config.project_name for project in reloaded.projects] == ["project1"]
+
+    def test_remove_project_preserves_concurrent_addition(self):
+        """A removal must not discard a project added by another config instance."""
+        p1 = self._make_project_dir("project1", 'project_name: "project1"\nlanguages: ["python"]\n')
+        p2 = self._make_project_dir("project2", 'project_name: "project2"\nlanguages: ["python"]\n')
+        p3 = self._make_project_dir("project3", 'project_name: "project3"\nlanguages: ["python"]\n')
+        self._write_master_config([p1, p2])
+
+        removing_config = SerenaConfig.from_config_file(generate_if_missing=False)
+        adding_config = SerenaConfig.from_config_file(generate_if_missing=False)
+        adding_config.add_project_from_path(p3)
+        removing_config.remove_project("project2")
+
+        reloaded = SerenaConfig.from_config_file(generate_if_missing=False)
+        assert {project.project_config.project_name for project in reloaded.projects} == {"project1", "project3"}
+
+    def test_add_project_preserves_concurrent_removal(self):
+        """An addition must not resurrect a project removed by another config instance."""
+        p1 = self._make_project_dir("project1", 'project_name: "project1"\nlanguages: ["python"]\n')
+        p2 = self._make_project_dir("project2", 'project_name: "project2"\nlanguages: ["python"]\n')
+        p3 = self._make_project_dir("project3", 'project_name: "project3"\nlanguages: ["python"]\n')
+        self._write_master_config([p1, p2])
+
+        removing_config = SerenaConfig.from_config_file(generate_if_missing=False)
+        adding_config = SerenaConfig.from_config_file(generate_if_missing=False)
+        removing_config.remove_project("project2")
+        adding_config.add_project_from_path(p3)
+
+        reloaded = SerenaConfig.from_config_file(generate_if_missing=False)
+        assert {project.project_config.project_name for project in reloaded.projects} == {"project1", "project3"}
+
 
 class TestGetRegisteredProjectWithDanglingProject:
     """A registered project whose root directory was deleted (e.g. a removed git