`deep-research` skill permanently disappears from autocomplete after a session hits usage limit mid-run (all other built-in skills unaffected)

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

The built-in deep-research skill vanished from Claude Code and has not returned.

Timeline:

1. In a session ~1 day ago, I invoked /deep-research.
2. That skill run spawned ~100 sub-agents and consumed my token/usage allowance very rapidly, hitting my usage limit and causing a HARD STOP mid-run. The spawned agents did not finish.
3. Since that session, deep-research no longer appears when I type /deep (autocomplete no longer offers it), and it is not invocable.
4. ALL OTHER built-in skills are still present and working (dataviz, artifact-design, verify, code-review, simplify, update-config, keybindings-help, fewer-permission-prompts, loop, schedule, claude-api). Only deep-research is gone.

What Should Happen?

A usage-limit hard stop should be transient. Once the usage limit resets, the deep-research skill should be available again. A skill should not be permanently removed from the account's available set as a side effect of hitting a usage limit during that skill's execution.

Error Messages/Logs

Steps to Reproduce

Not reliably reproducible on demand (would require intentionally exhausting a usage limit via a large agent fan-out). Observed sequence:

1. Run /deep-research <query> on a task that fans out into many sub-agents.
2. Let it run until it hits the account usage limit and hard-stops mid-run.
3. Start a new local session; type /deep — deep-research no longer autocompletes.

Claude Model

Not sure / Multiple models

Is this a regression?

Yes, this worked in a previous version

Last Working Version

2.1.207 (Claude Code)

Claude Code Version

2.1.207 (Claude Code)

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

VS Code integrated terminal

Additional Information

• Full native reinstall via irm https://claude.ai/install.ps1 | iex (user-scoped, completed successfully) — no effect.
• Confirmed claude --version = 2.1.207 after reinstall.
• Confirmed all other built-in skills still autocomplete and run.
• Reproduced the absence on a second, separate account on the same machine.
• Confirmed via a working environment (a Docker-based session where deep-research still functions) that the skill is NOT a loose file under ~/.claude/skills/ — it does not exist as a directory there even where it works, indicating it is delivered/gated server-side rather than shipped as a local file. This is why a binary reinstall does not restore it.