Cursor AgenThere have been multiple occurrences where Markdown files created with Cursor Agent and confirmed to exist in the IDE under ./documents seemed to disappear in subsequent sessions. Environment:
OS: Linux
Workspace: the specified workspace
Using Cursor Agent
File save location: ./documents
Confirmed to exist in the IDE immediately after creation
Later, files disappeared from the same ./documents directory. Similar issues with programs disappearing have occurred multiple times before. Issue:
Markdown records of research experiments disappeared, seriously affecting reproducibility and publication.
I would like you to check whether there are problems with the consistency between the Agent’s ApplyPatch/File tool/terminal operations and file display/persistence in the IDE.
Please let me know if there are any known issues on the Cursor side regarding file creation, deletion, restoration, synchronization, or checkpoints. Things I want to confirm:
Are there known issues where files created by the Agent disappear in subsequent sessions?
Is it possible that Agent tools and the IDE Explorer see different file system states?
Can checkpoints or chat/session restoration affect actual files?
What should I check in logs or diagnostic information?
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This falls into a known class of issues related to how Cursor’s checkpoint system tracks agent-created files. There are a few things that could cause this, and a couple of details would help us narrow it down.
The most common cause: when you edit or resubmit an earlier message in an Agent chat, Cursor rolls your workspace back to the state at that point. Files the Agent created after that checkpoint get removed, and in some cases this happens without a clear warning.
Could you share a few details?
Before the files disappeared, did you edit or resubmit a previous message in the Agent chat? This is the most common trigger for agent-created files being removed.
Are the files in ./documents tracked by git? If they’re untracked or in .gitignore, they can’t be recovered via git restore.
Did you close Cursor or put your machine to sleep between when the files existed and when they were gone? This helps us check a different known issue path.
Can you share a Request ID from the Agent session that created the files? (three dots menu in chat > Copy Request ID)
For prevention going forward:
Commit important files to git right after the Agent creates them. Even if a checkpoint restore removes them, git restore can bring them back instantly.
Be careful with editing earlier messages in an Agent chat after the Agent has created files you want to keep — this triggers a workspace rollback to that point.