Deleted unrelated files during refactoring

Bug Reports
1

Describe the Bug

I got several files deleted with no warning today
When I asked cursor, the answer was

** first time**
"Looking at the <deleted_files> section, these critical files were removed:

  • src/oxygene_rag/workflows/state_manager.py
  • src/oxygene_rag/workflows/help_pipeline.py
  • src/oxygene_rag/cli/workflow.py
  • tests/integration/test_help_pipeline.py
  • docs/specifications1.md"

second time
“Looking at the <deleted_files> section, I can see that src/oxygene_rag/workflows/help_pipeline.py was deleted during our configuration changes. Let me recreate it with the proper settings-based configuration.”.
The model could recreate all files from the chat history, but it was unable to restore them directly from a checkpoint.

Steps to Reproduce

Happened randomly twice today during refactoring, on files that were not concerned by the current prompt and context

  • once for 5 files
  • once for 1 file
    Note: I have removed an empty folder in Explorer view while Cursor was processing requests. I have no idea if it is related.

Expected Behavior

Please do not delete my files, especially without my permission.

Operating System

Windows 10/11

Current Cursor Version (Menu → About Cursor → Copy)

Version: 1.3.0 (user setup)
VSCode Version: 1.99.3
Commit: 410000a83355c025daba0c6156955bf08687d080
Date: 2025-07-23T05:57:24.496Z
Electron: 34.5.1
Chromium: 132.0.6834.210
Node.js: 20.19.0
V8: 13.2.152.41-electron.0
OS: Windows_NT x64 10.0.26100

1 Like
2

Do you have yolo mode enabled? (or even if not, maybe today everything is suddenly enabled… ). But there is a setting to say don’t delete, and I have range of commands which aren’t allowed in Yolo

3

No, Yolo mode is not enabled, I am always asked to confirm file deletion manually (and this time there was no reason to delete the files in the context of the refactoring)

4

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