MCP server functionality broken with Claude Desktop version: 1.12603.1

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?

Claude Desktop v1.12603.1 (Windows) silently strips the mcpServers block from claude_desktop_config.json on every launch, preventing any user-configured MCP servers from loading.

What Should Happen?

Hello Anthropic Support,

I am filing a bug report regarding a regression in Claude Desktop that broke MCP server functionality following the June 11, 2026 auto-update, and which persists even after attempting a rollback.

Environment:

• Claude Desktop version: 1.12603.1 (auto-installed June 11, 2026)
• Previous working version: 1.11847.5 (June 9, 2026)
• OS: Windows 10/11
• MCP Server: mcp-atlassian (Jira Data Center v10.3.2, self-hosted)

Issue:
Following the June 11 auto-update, Claude Desktop completely ignores the mcpServers block in claude_desktop_config.json. The MCP server (mcp-atlassian) was working correctly on May 12, 2026 and stopped functioning after the update.

Symptoms:

1. The mcpServers block is silently stripped from claude_desktop_config.json on every launch — the app actively overwrites the file, removing all MCP server configuration.
2. main.log shows repeated "Config file written" entries confirming the app is overwriting the config on startup.
3. main.log contains zero MCP-related entries — the server is never attempted.
4. Settings → Developer shows no MCP servers loaded.
5. No error messages are surfaced to the user — the failure is completely silent.

Steps to Reproduce:

1. Install or update to Claude Desktop v1.12603.1 on Windows.
2. Add a valid mcpServers block to %APPDATA%\Claude\claude_desktop_config.json.
3. Fully quit and relaunch Claude Desktop.
4. Observe that the mcpServers block has been removed from the config file.
5. Confirm via Settings → Developer that no MCP servers are registered.

Rollback Attempt — Also Failed:
I attempted to roll back to v1.11847.5 by directly launching the older executable:

& "$env:LOCALAPPDATA\AnthropicClaude\app-1.11847.5\claude.exe"

The rollback did not restore MCP functionality. The mcpServers block continues to be ignored and overwritten even when running the older version executable, suggesting the config overwrite behavior may be tied to shared app data or a registry entry that persists across versions.

Verified Not a Configuration Issue:

• PAT token independently verified as valid via PowerShell REST API call (200 OK)
• uvx.exe path verified correct via 'where uvx' and direct file check
• JSON config validated as syntactically correct
• JIRA_EMAIL removed per Data Center requirements (PAT auth only)
• TOOLSETS=all added per deprecation warning in mcp-server log
• MSIX virtualized path (AppData\Local\Packages\Claude_*) does not exist on this machine
• Issue is 100% reproducible across multiple relaunches, config rewrites, and fresh chat sessions

Requested Action:

1. Investigate the config file overwrite behavior introduced in v1.12603.1
2. Restore the ability for user-defined mcpServers entries to persist and load correctly on Windows
3. Clarify whether the config file location has changed in v1.12603.1 and document the correct path
4. Investigate why the rollback to v1.11847.5 did not restore prior behavior

Thank you,

Error Messages/Logs

any error message to include with bug report?

6:00 AM
Yes — include this key evidence from the logs:

From main.log:

"Config file written" — appears repeatedly, confirming app overwrites config on every launch
Zero MCP-related log entries — server is never attempted
From mcp-server-mcp-atlassian.log:

Server starts and connects successfully
"tools/list" returns {"tools":[]} — empty tool list
No auth errors, no crash — silent failure
The most telling error sequence:

Message from client: {"method":"tools/list"...}
Message from server: {"id":1,"result":{"tools":[]}}
That combination — successful startup but empty tools — followed by the config being overwritten on relaunch is the smoking gun. Include both log files as attachments if GitHub allows it.

Steps to Reproduce

Steps to Reproduce:

Confirm Claude Desktop auto-updated to v1.12603.1 on June 11, 2026
Fully quit Claude Desktop
Open %APPDATA%\Claude\claude_desktop_config.json in Notepad
Add a valid mcpServers block (example below) and save
Verify the block saved correctly via PowerShell: Get-Content "$env:APPDATA\Claude\claude_desktop_config.json"
Launch Claude Desktop
Immediately re-run the PowerShell command from Step 5
Observe that the mcpServers block has been stripped from the file
Open a new chat — confirm no MCP tools are available in Settings → Developer

Example mcpServers block used:
json"mcpServers": {
"mcp-atlassian": {
"command": "C:\\Users\\[username]\\.local\\bin\\uvx.exe",
"args": ["mcp-atlassian"],
"env": {
"JIRA_URL": "https://[your-jira-instance]",
"JIRA_PERSONAL_TOKEN": "[valid-PAT]",
"TOOLSETS": "all"
}
}
}
Expected result: mcpServers block persists after relaunch and MCP tools load in new chat sessions.
Actual result: mcpServers block is silently removed. No error is surfaced. MCP tools never load.

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

v1.11847.5

Claude Code Version

Claude Desktop for Windows, v1.12603.1.

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

PowerShell

Additional Information

NOTE!! upgrade was forced, not approved.
Rollback doesn't work.

URGENT.