some will drift back. as long as you gave both plenty of brood in all stages, you should be ok. if you find that there is to much drift, just swap the box positions. recheck the hives in a couple of weeks or so, you should be able to tell where the queen is, if she's still there. if you don't find eggs in either, don't panic.
since you found queen cells, it is possible that one already hatched out and the old queen was killed. just keep an eye on them so that you are sure that both end up with laying queens.