Need Support to purge dangling refs/pull/1/head after a completed git filter-repo scrub

[Sublx8ed01]

🏷️ Discussion Type

Question

Body

Repo: Sublx8ed01/chiro-backbone (private)

PHI (patient radiology files) was committed 2026-04-15 (commit
8c60bddaa8c6ec9f570d180f41d50c5f2ec9c4fb) and has since been removed via
git filter-repo, force-pushed 2026-07-02. Old pre-scrub main tip was
093b05d6200efec4e91012148722383e93a98c3e.

The rewrite is confirmed clean on all branches (fresh mirror clone shows
zero references to the removed content). However, refs/pull/1/head
(confirmed via git ls-remote, SHA 5c8f28bd4401b31b4a30f7497d3da3a2510a2e6a,
confirmed ancestor of the PHI commit) still pins pre-scrub history
server-side, so the removed PHI remains fetchable via that ref.

Number of affected pull requests: 1

I can't find a working ticket/form path through the current
support.github.com self-serve flow for this request type. Could someone
point me to the right process, or handle directly?

Requesting:

1. Delete/update refs/pull/1/head
2. Server-side GC of dangling commits, especially 093b05d... and 5c8f28b...
3. Purge any cached views/diffs referencing the removed content

[Vaishnavi252-ai]

It sounds like you've already completed the repository rewrite correctly by removing the sensitive content, force-pushing the cleaned history, and verifying that no branch or tag references the affected commits.

The remaining refs/pull/* references are GitHub-managed internal references and can't be deleted or updated by repository administrators. If those refs still expose the sensitive commits, this requires intervention from GitHub Support.

Since this involves sensitive data (PHI), I recommend contacting GitHub Support directly and clearly stating that you've already rewritten the repository history and that internal pull request refs are still retaining the removed commits. Include the affected repository, the pull request ref (refs/pull/1/head), and the commit SHAs you've identified, as you've done here.

GitHub Support can evaluate whether the pull request refs, cached diffs, and any server-side objects need to be purged. Because this concerns sensitive information, they generally handle these requests through the support team rather than the community forum.

Hopefully they can point you to the appropriate internal process or escalate the request for repository garbage collection and cache invalidation.

[lusker1]

Here is the technical solution to completely purge dangling pull request references and clear the server-side cache after running git filter-repo:

1. The Reality of GitHub's Architecture
   On GitHub, refs/pull/* references are read-only and managed strictly by GitHub's internal architecture. Even if you run git gc locally and force-push, standard Git commands cannot delete or modify remote PR references.

2. Solution A: The Official Approach (GitHub Support)
   If you want to keep the repository, issues, and stars intact, you must contact GitHub Support. Open a ticket and use the following template to request a server-side purge:

3. Solution B: The Nuclear Option (Self-Serve)
   If you cannot wait for support and want an immediate fix, you can completely overwrite the remote infrastructure by doing the following:

Delete the remote repository from your GitHub settings.

Create a brand new empty repository with the exact same name on GitHub.

Clean your local repository cache entirely to ensure no traces remain locally:

git reflog expire --expire=now --all
git gc --prune=now --aggressive

Force-push the clean history to the new repository:

git remote set-url origin git@github.com:Sublx8ed01/chiro-backbone.git
git push origin --force --all
git push origin --force --tags