[BUG] Config not persisting between sessions — theme + auth prompt every startup (Windows)

Bug Description

Every time I start a new Claude Code session, I'm prompted to:

1. Choose dark or light mode
2. Choose login method (subscription vs API token etc.)

These settings should persist but are lost between every session.

Evidence

~/.claude.json shows "numStartups": 1 despite hundreds of sessions — the config file is being read but never written back. Theme preference is completely absent from the file.

The config file is 5KB while a backup from Jan 28 is 8.8KB, suggesting data was lost/truncated at some point.

Environment

• Claude Code version: 2.1.62
• OS: Windows 11 Pro (10.0.26200)
• Shell: Git Bash
• Auth type: OAuth / Stripe subscription

Steps to Reproduce

1. Start Claude Code CLI
2. Choose theme (dark/light) and authenticate
3. Exit session
4. Start a new Claude Code session
5. Prompted again for theme and auth method

Expected Behavior

Theme and auth selection should persist in ~/.claude.json across sessions.

Additional Context

• ~/.claude.json has oauthAccount data with correct subscription info, but the startup flow still prompts for selection
• Possibly related to #1676 (config loss / race conditions)
• File permissions are fine (rw-r--r--)