[BUG] Claude Desktop silently overwrites claude_desktop_config.json with preferences-only stub, destroying all MCP server configuration (Linux)

Bug Report: claude_desktop_config.json silently wiped and replaced with preferences stub

Environment

• Platform: Linux (Ubuntu 25.10, GNOME, Wayland)
• Claude Desktop version: Latest (installed via claude-desktop-debian wrapper, running natively with CLAUDE_USE_WAYLAND=1)
• Installation method: .deb package (claude-desktop-debian)

Description

Within the space of approximately 1–1.5 hours this evening, claude_desktop_config.json was silently overwritten twice, replacing a fully-configured file containing 36 MCP server definitions with only the following stub:

{
  "preferences": {
    "coworkWebSearchEnabled": true,
    "coworkScheduledTasksEnabled": true,
    "ccdScheduledTasksEnabled": true,
    "sidebarMode": "chat"
  }
}

All mcpServers entries were completely removed with no warning, no error, and no backup created. Claude Desktop continued running without indicating anything was wrong — the MCP tools simply became unavailable.

Steps to Reproduce

1. Configure claude_desktop_config.json with multiple MCP servers (manually edited)
2. Run Claude Desktop (Wayland, Linux)
3. Use Claude Desktop normally — the file is silently overwritten within the session

Observed to occur twice within ~90 minutes.

Expected Behavior

claude_desktop_config.json should never have its mcpServers block removed by the application. If the preferences system needs to write to the file, it should merge/append rather than replace.

Actual Behavior

The entire file is replaced with a preferences-only stub. All MCP server configuration is lost. No warning is shown to the user. No backup is created.

Workaround

Setting the file read-only prevents the wipe:

chmod 444 ~/.config/Claude/claude_desktop_config.json

This is obviously not a sustainable solution as it prevents legitimate config updates.

Related Issues

This appears related to the new Cowork/extension management system introduced in v1.1.3189+ (build 2026-02-14). Similar conflicts have been reported:

• #31864 — Auto-update creates silent MCP extension conflict (Windows)
• #27492 — Cowork MCP registry connection failures after auto-update to v1.1.3189+

The preferences keys left behind (coworkWebSearchEnabled, coworkScheduledTasksEnabled, ccdScheduledTasksEnabled, sidebarMode) suggest the Cowork preferences writer is overwriting the entire file rather than merging its keys into the existing JSON structure.

Impact

Any Linux user with a manually-configured claude_desktop_config.json (the only supported method for MCP configuration on Linux) is at risk of silent, unrecoverable loss of their entire MCP server configuration. For users with complex configurations (36 servers in this case), restoring from backup is the only recovery path — and the second overwrite occurred after a backup was restored, meaning the bug is reproducible and persistent within a single session.