First year beekeeper here, bought my bees from BeeWeaver with a clipped queen. They really took off this summer and I was able to split the hive and take honey from the original hive. They put up a lot, what appears to be enough for them to overwinter on with little or no help from me. The second hive appears to be doing very well and have requeened themselves and put away some honey, though I'll have to help feed them through their first winter.

The issue is with the original hive, first they got invaded by some wasps who took over a section of their hive. Those are gone now. Then in August/September I was on the watch as it appeared they were becoming overrun with varroa. Moved the hives to the basement in October and have continued to keep a close eye on them. I know it isn't necessary to overwinter them indoors, but this hive has me scratching my head. Shortly before moving it indoors the bees were no longer on guard at the entrance and they could be seen dumping a few dead bees outside the hive. I chalked it up to perhaps something to do with a varroa problem.

Since being moved indoors they began dying off in hoards. The floor in my basement quickly became littered with drones that the workers were throwing out and other workers who would wander about but couldn't (or wouldn't) fly. Found the posts about the "Zombie" flies so I've collected a few bees who were wandering or swarming the light downstairs and am keeping an eye on them to see if anything emerges.

I opened the hive yesterday morning and am wondering if anything I observed is a sign of something else amiss. I believe this original hive is now queenless. There are many queen cells in various stages of assembly, but all are empty. In fact all the brood cells are empty, there is ZERO brood in the entire hive. I went through every comb and nothing, nada. They have a LOT of honey, but only a few cells on one comb have any pollen stores. Late summer when I went through the hive almost half of their food stores was pollen itself. Is this unusual for either scenario - too much or too little pollen stores?
Also, the hive is quiet. Normally when I'd open it there is a certain level of humming going on between the bees, this was dead silence... except the bees draw to the light while I was working - they were humming like crazy and in a bit of a frenzy over getting to the light. There were no guard bees to come and meet me while I was working, it was like they didn't know I was there.

I was happy to see that once I opened the hive many of the bees are moving about vs random wandering look. But, I also saw bees "walking in place", that is moving their legs but not going anywhere, and their abdomen was oddly risen in the air, looked as if it was filled with helium and they were trying not to float away. Dead bees on the bottom of the hive, though not as many as I was expecting, and some of the workers were still cleaning the hive of the dead bees. I did not identify as single drone in the hive, nor was I able to find the queen. Saw NO varroa in the hive, no deformed wings among the bees, etc.

Questions : I think I already know the answer, but is it too late in the year to order a new queen for this hive? Would it even be worthwhile? I've read the postings I could find about the Zombie flies, is there a treatment if that is what I'm dealing with? Should I consider recombining the two hives, since it appears the second hive is queened and healthy, or would that be too big a risk at ruining both hives trying to save the first?