A directory deletion arrives as ONE event on the directory's own path. That path has no source extension, so handleChange dropped it at the isSourceFile gate before ever scheduling a sync — and the files inside may never get events of their own (Windows's recursive watcher reports only the top-most removed entry; FSEvents can coalesce a tree deletion the same way). Every child record then sat stale in the index until an unrelated edit happened to trigger a sync (#1285). A non-source path that no longer EXISTS on disk now schedules the debounced sync; the sync's scan-diff removes whatever vanished (already correct — verified: manual `codegraph sync` cascades fine). Events for live non-source files stay fully ignored, so build churn schedules nothing. Fixes #1285 Co-authored-by: Claude Fable 5 <noreply@anthropic.com>