Fix: overlapping document parse race that can clear chunks (#13900)

### What problem does this PR solve?

This PR fixes a race in batch document parsing where overlapping parse
requests for the same document could clear/rewrite chunk state and make
previously parsed content appear lost. It adds an atomic per-document
parse guard so only one parse can run at a time for that document (Fixes
#13864 ).

### Type of change

- [x] Bug Fix (non-breaking change which fixes an issue)

test/testcases/test_http_api/test_file_management_within_dataset/test_doc_sdk_routes_unit.py

@@ -747,14 +747,14 @@ class TestDocRoutesUnit:
         monkeypatch.setattr(module.DocumentService, "query", lambda **_kwargs: [_DummyDoc(run=module.TaskStatus.RUNNING.value)])
         monkeypatch.setattr(
             module.DocumentService,
-            "update_by_id",
-            lambda *_args, **_kwargs: (_ for _ in ()).throw(AssertionError("update_by_id must not be called for running docs")),
+            "filter_update",
+            lambda *_args, **_kwargs: 0,
         )
         res = _run(module.parse.__wrapped__("tenant-1", "ds-1"))
         assert "currently being processed" in res["message"]
 
         monkeypatch.setattr(module.DocumentService, "query", lambda **_kwargs: [_DummyDoc(progress=0)])
-        monkeypatch.setattr(module.DocumentService, "update_by_id", lambda *_args, **_kwargs: True)
+        monkeypatch.setattr(module.DocumentService, "filter_update", lambda *_args, **_kwargs: 1)
         monkeypatch.setattr(module.DocumentService, "get_by_id", lambda _id: (True, _DummyDoc()))
         monkeypatch.setattr(module.File2DocumentService, "get_storage_address", lambda **_kwargs: ("b", "n"))
         _patch_docstore(monkeypatch, module, delete=lambda *_args, **_kwargs: None)