Serena notifies language servers about files changed outside its own edit tools (a git checkout, another editor, a build step) by sending workspace/didChangeWatchedFiles from LanguageServerManager.poll_and_notify, whose docstring names this exact case: such edits are 'otherwise invisible to a warm language server, causing symbolic queries to answer from a stale index'.
ClojureLSP never declared the corresponding client capability, so clojure-lsp was not told those notifications are sent and need not treat them as a reason to invalidate its analysis. DefaultInitializeParamsBuilder does not supply a default capabilities block, so nothing filled this in on the server's behalf.
Relates to #1593, where find_symbol returned a body from a comment mentioning the symbol rather than its definition, at a position the symbol had previously occupied.
