Hey @Serg_Ann, thanks for the report!
Restore Checkpoint only undoes edits the agent made with its file-editing tools. Changes it made by running terminal commands (like a Python or sed script) or through subagents, and edits you made yourself, stay in place.
If files the agent edited directly still don’t roll back, could you open View > Output, pick Cursor Composer from the dropdown, click Restore Checkpoint, and paste the lines that appear here along with the names of the files that stayed changed?
Until then, committing before an agent session is the most reliable way to roll back.