Permission settings reset after usage limit pause

Description

When Claude Code hits a usage limit and the session pauses waiting for it to resume, the permission settings reset to asking for approval on every tool call — even when bypassPermissions mode is configured.

Steps to Reproduce

1. Configure settings.json with:

{
  "permissions": {
    "defaultMode": "bypassPermissions"
  },
  "skipDangerousModePermissionPrompt": true
}

1. Use Claude Code normally (permissions are bypassed as expected)
2. Hit a usage limit — session pauses
3. Wait for the limit to reset and resume the session
4. Claude Code now asks for permission on every tool call as if bypassPermissions was never set

Expected Behavior

Permission settings should persist across usage limit pauses. If bypassPermissions is set in settings.json, it should remain active when the session resumes.

Actual Behavior

The session returns to asking for tool permissions after resuming from a usage limit pause. Running /permissions and re-selecting bypass mode fixes it for the rest of that session, but this shouldn't be necessary.

Environment

• Claude Code version: 2.1.86
• OS: CachyOS (Arch Linux), kernel 6.19
• Shell: fish