diff --git a/src/upload_handler.py b/src/upload_handler.py
index ba54219..0937a14 100644
--- a/src/upload_handler.py
+++ b/src/upload_handler.py
@@ -512,11 +512,23 @@ class UploadHandler:
         existing_key = None
         with self._index_lock:
             existing_files = self._load_upload_index()
+            stale_keys = []
             for key, info in existing_files.items():
                 if info.get("hash") == file_hash and info.get("owner") == owner:
-                    existing_key = key
-                    existing_file = info
-                    break
+                    stored_path = info.get("path")
+                    if stored_path and os.path.exists(stored_path) and self._inside_upload_dir(stored_path):
+                        existing_key = key
+                        existing_file = info
+                        break
+                    stale_keys.append(key)
+            if stale_keys:
+                for key in stale_keys:
+                    existing_files.pop(key, None)
+                try:
+                    self._atomic_write_json(uploads_db_path, existing_files)
+                    logger.info("Removed %d stale upload index entries for missing duplicates", len(stale_keys))
+                except Exception as e:
+                    logger.warning(f"Failed to remove stale upload index entries: {e}")
         if existing_file:
             logger.info(f"Duplicate file upload detected: {original_filename} -> {existing_file['id']}")
 
diff --git a/tests/test_upload_handler_atomicity.py b/tests/test_upload_handler_atomicity.py
index ceea9f0..73cf279 100644
--- a/tests/test_upload_handler_atomicity.py
+++ b/tests/test_upload_handler_atomicity.py
@@ -339,6 +339,37 @@ def test_smoke_duplicate_upload(tmp_path):
     assert len(final) == 1, f"Duplicate upload should not add a new row, got {len(final)}"
 
 
+def test_duplicate_upload_ignores_stale_missing_file(tmp_path):
+    """A stale uploads.json row should not make a new upload point at a
+    file that cleanup already removed from disk."""
+    handler = _make_handler(tmp_path)
+    handler.upload_rate_limit = 100
+    content = b"same-content-after-cleanup"
+
+    first = handler.save_upload(
+        SimpleNamespace(filename="cleanup.txt", file=io.BytesIO(content)),
+        "127.0.0.1",
+        "owner_a",
+    )
+    os.remove(first["path"])
+
+    second = handler.save_upload(
+        SimpleNamespace(filename="cleanup.txt", file=io.BytesIO(content)),
+        "127.0.0.1",
+        "owner_a",
+    )
+
+    assert second.get("is_duplicate") is not True
+    assert second["id"] != first["id"]
+    assert os.path.exists(second["path"])
+
+    with open(_db_path(handler), "r", encoding="utf-8") as f:
+        final = json.load(f)
+    ids = {row.get("id") for row in final.values()}
+    assert first["id"] not in ids
+    assert second["id"] in ids
+
+
 def test_smoke_info_lookup_after_bak_recovery(tmp_path):
     """Smoke test: after a torn write is recovered from the ``.bak`` sibling,
     ``get_upload_info`` still finds the original entry by id."""