kurt, i don't know if you have done many removals? there is a whole section on honeybee removal on here.
i am not a fan of leaving the top hive with no ventilation when i combine. if you are not sure you got the queen and worried about them leaving, at least give them a screened bit on the top of the hive. i have an old window screen that i use. it's held down with bricks and the top cover over it for rain/wind protection. it only takes a couple of days at the most for the hives to combine and you can take the screen off.
chances are, if you have gotten good bits of brood, they won't leave anyway. be careful about the honey. the smell of that will cause a robbing mess. i usually put a tarp about 100 ft from my hives and dump my scrap comb from the cut out on it. whatever is there, the bees will clean up and not (hopefully) be attacking each others hives.
another thing to consider for the future: if your primary goal in doing cutouts is to save the hives, you may have to set an end date to when you will do them. i am still getting calls, but i have to tell people that i will not be doing any more until spring. i know my odds of saving the hives at this time of the year are slim. i refer them to another who will do it for the money, or tell them to call me in the spring.
take pics!! good luck :-D