Hey, thanks for the report. This is a known bug with diff rendering. When the agent makes edits and the diff doesn’t show correctly, the Keep and Undo buttons don’t appear, and reverting to a checkpoint breaks. The chat looks reverted, but the files stay modified.
More details and the main thread: Keep / Undo buttons missing and “Discard to checkpoint” not reverting changes
Workaround: make a git commit before big agent sessions. If checkpoint revert doesn’t work, you can always roll back with git checkout -- . or git stash.