i’ve had a similar problem on a couple of occasions, here’s the most recent:
two tracks. four takes. exactly the same length, in the correct lane order (1,2,3,4). then i created a folder, brought both tracks in, engaged group edit. the “not in sync” warning did NOT come up. i made a few cuts. which cut fine, across all takes on both track…but then as soon as i started selecting segments from the different takes it gets all scrambled/shuffled up.
i’ve had it happen to groups tracks where there has ended up been a difference in length, or especially if one track was briefly/accidentally disabled during tracking. also, one time it seemed to solve the problem when i showed lanes on all of the tracks (which is ridiculous if that really was the solution). i dunno, just seems buggy or unrefined? and quite the frustrating bummer.