Hey @AcidDiz,
A restore only reverts files the agent edited with its own edit tools. Anything a terminal command, a subagent, or you changed by hand stays under Changes, and .ipynb files aren’t restored. It reverts files only, not the chat, which is why the earlier message just becomes editable. (Checkpoints docs.)
If files the agent itself edited are staying behind, next time it happens grab this before anything else: Help → Toggle Developer Tools → Console, click Restore Checkpoint, filter for [composer], and paste the lines plus the file names that stayed. No original file state found or an error line tells us exactly what happened.
Reliable fallback meanwhile: commit before an agent session. To clear leftovers, git checkout -- <file> or git stash discards them — those throw away the uncommitted changes, so check the file list first.