You ask an agent to organize or clean up files and it removes far more than you meant. Reports include a whole home folder, 11GB of demo files, and a folder of about 15 years of family photos. Files removed by a shell command skip the trash, so there is often nothing to restore.
The reported cases share a few patterns. A delete command picked up an extra path (a trailing ~/ in one Claude Code case). A move into a folder that was never created overwrote file after file (the Gemini CLI case). A delete that the user approved for "temporary files" also caught a real folder (the Cowork photo case). In each case the user either approved the step or ran with checks relaxed.
Back up the folder before you start. Tell the agent it may only create folders, move files and rename files, and that junk goes to a _REVIEW folder for you to delete by hand. Ask it to check that each target folder exists and each target name is free, to log every move, and to recount files after each batch. Keep the agent in the mode that asks before acting, read every delete prompt in full, and never run a terminal agent with permission checks turned off on a real machine. For Claude Code, add a deny rule for rm in your permissions.
The poster asked Claude Code to clean up packages in an old repository. The log they shared shows an rm -rf command that ended with ~/, which removed their home folder, including the Desktop, Keychain and Claude credentials.
The poster says Cowork ran an irreversible rm -rf during a recorded demo and deleted 11GB of files, which he says were not important.
Nick Davidov says he approved a Cowork request to delete temporary Office files while organizing a desktop, and a folder of about 15 years of photos was deleted too. With no Time Machine backup, he got the files back with help from Apple and iCloud.
The user asked Gemini CLI to organize files in its folder and reports that it lost them. The AI Incident Database entry says a folder was never created and later moves overwrote all but one file.