The general consensus seems to be that when doing a cutout you should put the bees and brood into a hive box(s) and leave it there, open, so any bees you missed will be able to join the main colony. This presumes you have the queen in the box, I believe.
If you do this what is to prevent the queen and all of the bees absconding? Or is this just a risk you take? How often does it happen, in your experience?
Why not just close up the hive for a few days while they acclimate and begin to feel at home? If you leave it in the vicinity of the cutout the missing bees might last until you open the hive again.