Man, the more I learn, the less I know. By accident, I located my marked queen this afternoon, the one I thought had been superceded.
The colony is doing well in spite of my "help." They are drawing comb and storing nectar in the second honey super, and have filled much of the first super with honey. There's still a lot of brood in the first super, from when the queen was in there laying. But about six frames are all honey, although not all of it is capped. So my plan to spin off some honey today will have to wait a while yet.
So I went into the lower boxes to see what was going on in them. The upper brood box still had many frames of capped honey, with most of the rest capped and uncapped brood. In the bottom box I found that the bees were collecting a lot of many different colors of pollen. There was also honey stored on the outer frames, and the rest a whole lot of empty comb. That's where I found my old marked queen, walking on the comb and looking to lay more eggs. Jeez, I hadn't seen her for two months, and thought she was long gone.
The inspection was much calmer today. I took extra care to pull the frames straight up and crushed very few in the process; they seemed to like that much better.
Probably why I was able to get all the way into the hive and find the queen that I'd been missing for so long.
The more I know, the more I need to learn. Hey, soon I'll be learning about over-wintering!