I removed the bottom and inverted the squirrel-house hive about 3 weeks ago. Cut a hole in a piece of plywood and sat a hive body with some drawn comb above it. I used a top shim with entrance hole to force the bees to crawl across the combs. Yesterday, I checked them and they have only a small amount of brood, and only a little very dark honey, and only a few handsful of bees.
I opened the box, cut the combs and installed them in a medium with some permacomb. I also found several empty queen cells, but didn't find a queen, although I didn't look too hard.

This AM, the bees are active, but I'm thiking they are being robbed. I'll probably end up combining this hive with a large swarm I caught Sunday PM. I doubt they'll have much to do with the permacomb at this point, so I will end up just throwing out the natural comb after the bees die out.