GitHub Merge Queue Silently Reverted Code

Tip: identify PRs with this problem by looking for discrepancies between the metadata (files/lines affected) for PRs via GitHub API and associated commits in the time window.

This was a pain to clean up!

Might want to check your git logs if you are using the Merge Queue feature. This afternoon, we found that Merge Queue was silently reverting changesets in the merge queue. Acknowledged by GitHub, but could be a very hard problem to debug if you aren't looking for it.

The window to audit is 2026-04-23 16:05 to 20:43 UTC, about 4h 38m, and 'merged incorrectly' is unpacked in exactly no detail on the status page. Practical check is to compare the tree of each merge commit in that window against the tree of the rebased-and-tested commit that the queue ran CI on. GitHub Enterprise Cloud with Data Residency is still affected as of the latest status update, so DR customers shouldn't clear new queue merges yet. Would be kinda useful if GitHub published the specific failure mode, because content-drift and parent-linkage and dropped-changes all need different audit scripts.

This has caused a morning of fun for our team, how do you break one of the most fundamental bits of your system? Time to look at alternatives...

for other folks currently in an incident trying to resolve the chaos this caused, the first commit we've found with issues in our repo is from ~10:30am pacific this morning