Auto-update deletes session .jsonl files, wiping token usage history and conversation data

Summary

Claude Code auto-updates are silently deleting session .jsonl files from ~/.claude/projects/ directories, resulting in permanent loss of conversation history and token usage data. The /stats dashboard shows drastically reduced totals because it can only read surviving files.

Evidence

Environment: macOS, Claude Code 2.1.87, upgraded through multiple auto-updates since Jan 2, 2026.

Two batch deletion events observed

Event 1 — Mar 25, 10:43:20
All .jsonl session files deleted from older project dirs (-Users-andrew-Documents-Coram-repos-*). Every directory under these paths received the exact same mtime, indicating a single batch operation.

Event 2 — Mar 30, 10:51:58
Same pattern on newer project dirs (-Users-andrew-Documents-work-coram-code-*). This occurred exactly 10 minutes after Claude Code 2.1.87 auto-installed at 10:41:29.

What was lost

• 520 out of 520 sessions referenced in sessions-index.json files have their .jsonl files missing
• 282 session directories exist with only subagents/ data inside — the main conversation .jsonl is gone
• Session dates span Jan 2 – ~Mar 1, 2026 — roughly 2 months of daily heavy usage
• /stats shows 13.7m tokens (from ~1 month of surviving data); actual usage was likely 30m+

What survived

• Session directories with subagent .jsonl files (11,207 files containing real token usage data)
• sessions-index.json files — still reference the deleted .jsonl paths with metadata (session summaries, message counts, dates, branches) but no token counts
• history.jsonl — prompt history going back to Jan 2
• Session .jsonl files dated Mar 2+ — these were apparently written by a newer storage format or path and were not targeted by the cleanup

Proof the files existed

The sessions-index.json entries contain fileMtime values corresponding to dates when the .jsonl files were last written (Jan–Feb 2026). These are not stale references from a format migration — the files were actively maintained and then deleted.

Example from sessions-index.json:

{
  "sessionId": "7ae2c6c3-acd8-4f61-baec-d467a21cbd9e",
  "fullPath": "~/.claude/projects/-Users-andrew-Documents-Coram-repos-logistics-app/7ae2c6c3-....jsonl",
  "fileMtime": 1769033018707,
  "messageCount": 57,
  "created": "2026-01-08T23:10:07.576Z",
  "summary": "LLM config Langfuse logging EDGE-898"
}

The fullPath .jsonl file no longer exists. The directory for this session ID also no longer exists. But the index proves the file was there.

Root cause (likely)

The session listing function (visible in the binary as Y79) scans for .jsonl files:

if(!O.endsWith(".jsonl"))return null

A cleanup or migration step during auto-update appears to delete .jsonl files from project directories it considers stale — possibly based on project path changes (the working directory path changed over time as repos moved). The cleanup does not update or remove the corresponding sessions-index.json entries, leaving orphaned references.

Impact

• Permanent, unrecoverable loss of conversation history
• /stats token counts are wrong (showing ~45% of actual usage)
• sessions-index.json files are orphaned tombstones
• No warning, no backup, no opt-out

Expected behavior

• Auto-updates should never delete session data without explicit user consent
• If a storage format migration is needed, old data should be migrated, not deleted
• At minimum, if cleanup is intentional, sessions-index.json should be updated to reflect the deletion

Versions affected

Cannot confirm exact version that introduced the cleanup, as older binaries are removed during auto-update. Observed across the upgrade path leading to 2.1.86 → 2.1.87 → 2.1.88.