I encountered the same problem today. 4 PRs in the stack, top of the stack is showing conflicts. Running through gh stack checkout and gh stack rebase all resolves and PRs are pushed up. I also tried gh stack sync with no success.

@LukGer I tried your suggestion to unstack, retarget, and restack. It worked perfectly.

First, I actually tried to unstack and restack without retargeting, and the same conflicts appeared, no success.

So, I took the top PR in the stack, retargeted it to main and then back to it's original target in the stack. Restacked it, and viola, no conflicts. Thanks. @LukGer

I unstacked and saw the same phantom merge conflict. Then I closed and reopened the PR twice and it went away.