diff --git a/scripts/remote_upload_client.py b/scripts/remote_upload_client.py
index a8e8a5be..ef66daf0 100644
--- a/scripts/remote_upload_client.py
+++ b/scripts/remote_upload_client.py
@@ -47,6 +47,25 @@
 import scripts.ingest_code as idx
 
 
+def _cache_missing_stats(file_hashes: Dict[str, Any]) -> Tuple[bool, int, int]:
+    """Return (is_stale, missing_count, checked_count) for cached paths."""
+    if not file_hashes:
+        return (False, 0, 0)
+    missing = 0
+    checked = 0
+    for path_str in file_hashes.keys():
+        try:
+            if not Path(path_str).exists():
+                missing += 1
+        except Exception:
+            missing += 1
+        checked += 1
+    if checked == 0:
+        return (False, 0, 0)
+    missing_ratio = missing / checked
+    return (missing_ratio >= 0.25, missing, checked)
+
+
 def _find_git_root(start: Path) -> Optional[Path]:
     """Best-effort detection of the git repository root for a workspace.
 
@@ -337,6 +356,24 @@ def _load_local_cache_file_hashes(workspace_path: str, repo_name: Optional[str])
         file_hashes = data.get("file_hashes", {})
         if not isinstance(file_hashes, dict):
             return {}
+        is_stale, missing, checked = _cache_missing_stats(file_hashes)
+        if is_stale:
+            logger.warning(
+                "[remote_upload] Detected stale local cache (%d/%d missing); clearing %s",
+                missing,
+                checked,
+                cache_path,
+            )
+            try:
+                cache_path.unlink(missing_ok=True)  # type: ignore[arg-type]
+            except TypeError:
+                try:
+                    cache_path.unlink()
+                except Exception:
+                    pass
+            except Exception:
+                pass
+            return {}
         return file_hashes
     except Exception:
         return {}
diff --git a/scripts/standalone_upload_client.py b/scripts/standalone_upload_client.py
index 979244ad..11f9cba3 100644
--- a/scripts/standalone_upload_client.py
+++ b/scripts/standalone_upload_client.py
@@ -155,7 +155,15 @@ def _load_cache(self) -> Dict[str, str]:
         try:
             with open(self.cache_file, 'r', encoding='utf-8') as f:
                 data = json.load(f)
-                return data.get("file_hashes", {})
+                file_hashes = data.get("file_hashes", {})
+                if self._cache_seems_stale(file_hashes):
+                    logger.warning(
+                        "[hash_cache] Detected stale cache with missing paths; resetting %s",
+                        self.cache_file,
+                    )
+                    self._save_cache({})
+                    return {}
+                return file_hashes
         except Exception:
             return {}
 
@@ -197,6 +205,21 @@ def remove_hash(self, file_path: str) -> None:
             file_hashes.pop(abs_path, None)
             self._save_cache(file_hashes)
 
+    def _cache_seems_stale(self, file_hashes: Dict[str, str]) -> bool:
+        """Return True if a large portion of cached paths no longer exist on disk."""
+        total = len(file_hashes)
+        if total == 0:
+            return False
+        missing = 0
+        for path_str in file_hashes.keys():
+            try:
+                if not Path(path_str).exists():
+                    missing += 1
+            except Exception:
+                missing += 1
+        missing_ratio = missing / total
+        return missing_ratio >= 0.25
+
 # Create global cache instance (will be initialized in RemoteUploadClient)
 _hash_cache: Optional[SimpleHashCache] = None
 
diff --git a/scripts/upload_service.py b/scripts/upload_service.py
index ad386faf..4807ef0f 100644
--- a/scripts/upload_service.py
+++ b/scripts/upload_service.py
@@ -175,6 +175,25 @@ def validate_bundle_format(bundle_path: Path) -> Dict[str, Any]:
     except Exception as e:
         raise ValueError(f"Invalid bundle format: {str(e)}")
 
+def _cleanup_empty_dirs(path: Path, stop_at: Path) -> None:
+    """Recursively remove empty directories up to stop_at (exclusive)."""
+    try:
+        path = path.resolve()
+        stop_at = stop_at.resolve()
+    except Exception:
+        pass
+    while True:
+        try:
+            if path == stop_at or not path.exists() or not path.is_dir():
+                break
+            if any(path.iterdir()):
+                break
+            path.rmdir()
+            path = path.parent
+        except Exception:
+            break
+
+
 def process_delta_bundle(workspace_path: str, bundle_path: Path, manifest: Dict[str, Any]) -> Dict[str, int]:
     """Process delta bundle and return operation counts."""
     operations_count = {
@@ -313,10 +332,23 @@ def process_delta_bundle(workspace_path: str, bundle_path: Path, manifest: Dict[
                         else:
                             operations_count["failed"] += 1
 
+                        # Remove original source file if provided
+                        source_rel_path = operation.get("source_path") or operation.get("source_relative_path")
+                        if source_rel_path:
+                            source_path = workspace / source_rel_path
+                            if source_path.exists():
+                                try:
+                                    source_path.unlink()
+                                    operations_count["deleted"] += 1
+                                    _cleanup_empty_dirs(source_path.parent, workspace)
+                                except Exception as del_err:
+                                    logger.error(f"Error deleting source file for move {source_rel_path}: {del_err}")
+
                     elif op_type == "deleted":
                         # Delete file
                         if target_path.exists():
                             target_path.unlink()
+                            _cleanup_empty_dirs(target_path.parent, workspace)
                             operations_count["deleted"] += 1
                         else:
                             operations_count["skipped"] += 1