diff --git a/plugins/disk-cleanup/disk_cleanup.py b/plugins/disk-cleanup/disk_cleanup.py
index bd07f844bb4eb..8432c5a7bad3b 100755
--- a/plugins/disk-cleanup/disk_cleanup.py
+++ b/plugins/disk-cleanup/disk_cleanup.py
@@ -148,6 +148,9 @@ _EMPTY_DIR_PROTECTED_TOP_LEVEL = frozenset({
     "logs", "memories", "sessions", "cron", "cronjobs",
     "cache", "skills", "plugins", "disk-cleanup", "optional-skills",
     "hermes-agent", "backups", "profiles", ".worktrees",
+    # User-authored project trees — never sweep empty directories
+    # inside these (#75403).
+    "patches", "projects", "skins", "themes", "contributors",
 })
 
 _EMPTY_DIR_SWEEP_PRUNE_DIRS = frozenset({
@@ -336,6 +339,21 @@ def quick() -> Dict[str, Any]:
                 # Drop the stale entry — it was misclassified.
                 continue
 
+        # ---- stale-state migration for 'test' category (fixes #75403) ----
+        # Old tracked.json entries may carry a "test" category for paths
+        # that are now under protected project directories (patches/,
+        # projects/, etc.).  guess_category() was tightened in the fix for
+        # #75403, but existing entries are never re-validated.  Re-classify
+        # here so stale entries for protected paths are not deleted.
+        if cat == "test":
+            re_cat = guess_category(p)
+            if re_cat != "test":
+                _log(
+                    f"SKIP stale test entry: {p} "
+                    f"(re-classified as {re_cat!r} — under protected tree)"
+                )
+                continue
+
         # Hard safety net: never delete cron control-plane state even if
         # the category somehow slipped through re-validation above.
         if _is_protected_cron_path(p):