Session cleanup deletes same-day sessions unexpectedly

Description

Sessions created on the same day are being deleted during startup cleanup, even though they should be retained based on the cleanupPeriodDays setting (default 30 days).

Environment

• Claude Code version: 2.1.12
• OS: macOS (Darwin 25.1.0)
• Platform: darwin

Steps to Reproduce

1. Start Claude Code and have several conversations throughout the day
2. Close terminal and reopen
3. Start a new Claude Code session
4. Run /resume - previous sessions are missing

Expected Behavior

Sessions created within the cleanupPeriodDays period (default 30 days) should be preserved and available via /resume.

Actual Behavior

All 5 sessions created the same day were deleted during startup. Debug logs show:

2026-01-17T18:16:05.137Z [DEBUG] Session index: added 1, updated 2, removed 0 (total: 5)
2026-01-17T20:19:27.848Z [DEBUG] Session index: added 0, updated 0, removed 5 (total: 0)

The cleanup at 20:19:27 removed all 5 sessions, despite them being created earlier the same day.

Additional Context

• cleanupPeriodDays was set to 36500 at 20:29:30 (after the cleanup had already run)
• However, even with the default 30-day retention, same-day sessions should not be deleted
• The history.jsonl file shows 8+ session IDs were used, but only 2 session files remained after the cleanup
• Sessions index file (sessions-index.json) went from 5 entries to 0 in a single startup

Debug Log Excerpt

From session 9d6e8a4a-cee8-41ae-be27-1a848fe3c74b.txt (the session that triggered the cleanup):

2026-01-17T20:19:27.843Z [DEBUG] [STARTUP] Running setup()...
2026-01-17T20:19:27.846Z [DEBUG] Stats cache is up to date
2026-01-17T20:19:27.846Z [DEBUG] Plugin autoupdate: skipped (auto-updater disabled)
2026-01-17T20:19:27.848Z [DEBUG] Session index: added 0, updated 0, removed 5 (total: 0)

The cleanup happened immediately during startup with no indication of why sessions were marked for removal.

Workaround

Setting cleanupPeriodDays to a high value (e.g., 36500) in ~/.claude/settings.json before any sessions are created may prevent this, but this does not explain why same-day sessions were deleted.