Claude Code changed files it shouldn't have. What to do right now

Do this first, in this order

1. Stop it. Interrupt the session. Don't let it "fix" its own fix.
2. Switch to Manual. Press Shift and Tab until the status line says manual. Now nothing runs without your yes.
3. Rewind this session. Press Esc twice, or type /rewind. Pick a point from before the change. This covers file edits made in this session.
4. Using git? Go back a step. Ask: "Show me the commits since last Monday. Restore the project to the one I choose." Pick it yourself.
5. See who did it. Ask: "Run git reflog and show me the last 20 lines. Explain each line in plain words. Change nothing."
6. Check online actions. Did it send, publish or change something on a website? No undo button covers that. Fix it at the service now.
7. Check with your eyes. Open the files that matter. Don't trust "restored" until you've looked.

The checkpointing page in the official docs lists exactly what rewind can and can't bring back.

Which rewind option to pick

When you press Esc twice (with the input box empty) or type /rewind, you get a list of the prompts you sent in this session. Pick the one from just before things went wrong. Then the checkpointing docs list these choices:

There are also two summarize options. They shrink the chat to save space and do not touch your files. If the code options are missing, Claude made no tracked file edits after that point.

What rewind cannot bring back

Rewind only knows about edits Claude made with its own file editing tools. The docs list the gaps:

• Files changed by terminal commands. If Claude deleted, moved or copied files with a command like rm, mv or cp, rewind cannot undo it. A git stash like the one in my story below is also a command. Use git or your backup for these.
• Edits made by helper agents. Rewind restores only files Claude had already edited in your own conversation. Anything else a helper agent changed stays changed. Use git.
• Changes from outside the session. Your own edits in another program, or another Claude session working in the same folder, are normally not tracked.
• Linked files. Files that are links to other files are skipped, and Claude Code tells you how many it skipped.
• Old sessions. Claude Code keeps snapshots for the 100 most recent checkpoints in a session, and deletes them about 30 days after the session last saved one.

That list is why the book gives you three undo buttons, not one.

Your folder just jumped back in time

You were in the middle of work. You open a file and it's the version from days ago. Or a dozen files are renamed. Nobody said yes.

Breathe. Most of the time, this is recoverable in minutes. The steps above are ordered from cheapest to biggest.

The helper that was told not to touch anything

In July 2026 I sent a review agent to check the code on one of my sites. The prompt said, in capital letters, READ-ONLY, do NOT edit.

It wanted to compare today's code with an older save point. So on its own it ran git stash, which tucks away unsaved changes and puts the files back to the last save. Then git stash pop to bring them back. To the agent, that was reading. It hadn't edited a single file.

But my main session was editing those same files at that moment. The whole folder jumped back in time, and for a few minutes nobody knew who had reset it.

The fix was two things. Every reviewer prompt now names each banned git command one by one. And reviewers get a tool list that takes the terminal away, so they can't run git at all. A sentence in a prompt is advice. A tool list is a lock.

On September 18, 2026, it was worse. A whole other website's files turned up inside one of my projects, about 1,500 untracked files and 370 tracked ones. Two AI tools had worked on the same disk. Git restored every tracked file in seconds. One local settings file had never been in git, and it was gone for good. Git only protects what's committed.

The chapters for the next time

This is the problem Claude Code for Non-Programmers was written for. The book is independent and is not affiliated with Anthropic.

Safety and Failure gives you the three undo buttons, a daily git routine of three lines, a weekly health check and a card called "Which undo do I need?" to tape by the screen.

Permissions and Modes sets Manual as your default and adds deny rules that hold in every mode. The permissions page is the source.

A Team of Agents has the reviewer rules and a helper file that truly can't write. Once the panic is over, read checking an agent's report before you act.