How can i recover these files back?
Why are you delegating such a critical task to an agent in that way, be responsible 
Advices:
- If your agents will work with a code base and assets, seed it to them from a single source of truth.
- Create a rule that specifies that previous to any bulk update/delete related task a check for a existing updated backup need to exists (your preference here: shelve changes, backup modified artifacts, etc.)
- Don’t let agents run scripts without reviewing them first. If possible call well known tools to clean those files.
- Treat your agents as employees, they WILL make mistakes.
- If you don’t want to work with an external repo you can create a bare repo in an out-of-tree folder and clone/commit there. Compressed files as a backup system is brittle unless used for archival. Even better if you can set all this in another device.
Hope all goes well.