Fork a project with unmerged checkpoints (“project a” > “project forked”).
Delete the forked project (“project forked”).
Merge the checkpoints in “project a”.
Fork the now merged project re-using the name (“project a” > “project forked”).
The new “project forked” will not reflect the merge.
I tried to recreate the issue and you’re right it can’t be recreated (at least this simply).
I think it may have been an issue with an older project I’ve since deleted which was also having issues with deleting branches due to checkpoint conflict.