Hey, thanks for the detailed report.
We’re already tracking the issue where undo deletes files instead of reverting changes. A few users have hit similar behavior in recent versions:
In your case there’s an important detail. It also affects SSH remote workspaces, where the agent session’s historical state leaks into the undo scope.
As a temporary workaround until we ship a fix, please make frequent commits before rolling back agent changes. That way git checkout or git restore can recover anything that gets deleted.
Let me know if you need anything else.