[BUG] Claude can't access a private personal GitHub repo despite Claude GitHub App being granted full access (backend index/sync issue)

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 claude.ai / Claude desktop GitHub integration cannot access a PRIVATE
repository on my personal account, even though the official Claude GitHub
App (github.com/apps/claude) is installed and has been granted access.

Account: F4UC (personal account)
Repository: F4UC/islamicfiqhpublishing (private)

What I have tried:

• Granted the Claude GitHub App access using "All repositories" AND

"Only select repositories" (with the specific repo selected). Saved each time.

• Disconnected and reconnected the GitHub Integration in the Claude app,

re-authorized the OAuth flow.

• Removed a conflicting custom GitHub MCP connector.
• Confirmed the repo exists and is healthy (visible under my Repositories

tab with a Private badge; it has recent commits and an open PR).

Key symptom — INTERMITTENT access:
At one point the repo became readable for a few minutes (a file fetch
succeeded), then it reverted to "404 Not Found" again with no settings
change on my side. A second private repo on the same account
(F4UC/-Transmission-Network) shows the same behavior. Public repos on the
same account work fine.

History that may be relevant:
This repo originally worked while private. It was then transferred to an
organization and later transferred BACK to my personal account. The access
problem started after the transfer back to personal.

This looks like the same backend indexing/sync issue reported in #33875,
#12839, #18467, and #27155 — personal-account private repos not being
correctly indexed on the backend even when the GitHub App has full access.

What Should Happen?

After granting the Claude GitHub App access to a private personal repo
(via "All repositories" or "Select repositories"), the repo should be
consistently accessible in Claude (Chat attach, Projects, and Code) without
intermittent 404s.

Error Messages/Logs

Steps to Reproduce

1. Have a PRIVATE repo on a personal GitHub account (bonus: one that was

transferred to an org and back).

1. Install/configure the Claude GitHub App (github.com/apps/claude) and

grant "All repositories".

1. In Claude, try to access the repo (Chat "Add from GitHub", Projects, or Code).
2. Observe: repo returns 404 / "Claude cannot access that resource",

intermittently succeeding then failing again.

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

N/A — Claude Desktop app (Max plan), GitHub connector issue, not Claude Code CLI

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

Requesting a backend repository index reset / re-sync for account F4UC.
References: #33875, #12839, #18467, #27155.
Platform: Claude desktop app (macOS) + claude.ai GitHub integration.
This is NOT a Claude Code CLI bug — it's the GitHub integration on the
account/backend side.