[Bug]: Deleting files from the knowledge base did not take effect

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### RAGFlow workspace code commit ID

1234

### RAGFlow image version

v0.20.1

### Other environment information

```Markdown
docker
```

### Actual behavior

I deleted a file in the knowledge base, but I can still query the relevant chunks of the deleted file through the interface. Is there a cache? What should I do?

### Expected behavior

_No response_

### Steps to reproduce

```Markdown
success
```

### Additional information

_No response_

No source file or test is named. First reproduce the knowledge-base deletion and query flow in the reported Docker environment, then trace how deleted file chunks remain searchable. Done means queries no longer return chunks from a deleted file, with a regression test covering the behavior.

Written by the indexing model from the issue text.