After a late September swarm, I had to combine my two hives as well. Isn't it fun doing all this fire fighting as a new beekeeper? As for agitation, my girls, gentle all summer, are now defensive, too. The foragers don't have anything to do but guard, so they're on the defensive, with all those stores to get them through winter, I guess.
I couldn't find the queen, either, and that didn't seem to inhibit things. It's been over a month now, and the combined hive is happily taking syrup for winter, and all seems well with the colony. I hope they'll get through winter and have a hive-busting spring build up so that I can split it back to two hives--though I plan to buy a few packages to increase the size of my "apiary."
So far, weather has been mild, so I haven't wrapped the hive, though I did put on a mouse guard--though with the girls being all pissy, I'd pity the mouse that tried to get into that hive!