I wouldn’t put the deep back on. The last thing bees need in the winter is a larger volume hive than necessary. When mine are really looking too crammed after removing the supers, I will put a 2” or 3” spacer on top the brood box for a month or so. The nice thing about a frameless spacer box is a volume of 2” x 19” x 15” (or whatever you’re running) will hold a LOT of bees since they can hang from the roof in big balls of bees.
This time of year, bees that get stuck hanging outside the hive will end up going off to bee heaven prematurely as the weather gets cold and rainy. Yes, a 2” empty spacer violates bee space, but the bees aren’t building comb this time of year in Michigan and probably not in Mass either. The spacer box also seems to allow the bees room to hang out and re-organize a bit before winter hits. Just an idea.
We had a light frost last night. Winter is on it's way to you.