My confidence is restored, bubble support got back to me. This is not a bug and it’s behaving as designed, and it makes sense.
They said:
"To provide some context on this, when deploying to Live from Main, the other branches do not track what was deployed but only that a deployment occured. So, that is why branch [mybranch]’ is ‘out of sync’ but has no changes or conflicts to resolve. While no changes were actually made, the branch does not know there were no changes made in Main before deploying. "
The latest community update also specifically mentions how a changelog is in the works.