Claude Code deletes 48,000 files in about 100 seconds and corrupts Git history
Reports say a Claude Code cleanup script deleted roughly 48,000 files in about 100 seconds on 28 September 2026 and corrupted the Git database. The agent only apologized; according to a SpecPilot analysis, the missing backup caused the irreversible damage.
Who is affected and how
- senior developer
- Run agents only on repositories protected by a remote backup, and require approval for destructive commands such as deletion or history rewriting.
- tech lead
- Set team-wide limits on agent permissions and make backups a requirement.
Sources
- AI coding agent deletes 48,000 files, corrupts Git databasetechgig · Sep 28, 2026
- AI coding agent deletes 48,000 files due to mishandled Windows junctionssc media · Sep 28, 2026
- AI coding agent deletes 48,000 files due to mishandled Windows junctions | brief | SC Mediascworld.com · Sep 28, 2026
- AI Coding Agent Deletes 48,000 Production Files — JournalArta Globaljournalarta.com · Oct 2, 2026
- "I broke something": Claude Code deleted 48,000 files in 100 seconds and simply apologized to the developerdev.ua · Sep 28, 2026
- Claude Code Deleted 48,000 Files. Here's How to Stop Itaitoolbriefing.com · Sep 28, 2026
- Claude Code Agent Deleted 48,000 Files in 100 Seconds: What Went Wrong — DiffVibediffvibe.com · Sep 30, 2026
- Claude Code Deleted 48,000 Files in 103 Seconds. The Missing Backup Did the Real Damage. | SpecPilotspecpilot.dev · Sep 29, 2026
Machine-generated summary based on the titles and excerpts of the source articles. The facts come from the linked article.