Biology of the Honey Bee

It's been nearly two weeks since I'd been into the hive. It was partly overcast and warm today. The bees were calm throughout the entire inspection, which was a bit long. I hope my girls didn't get too cold. I've read that if the inspection takes long, the beekeeper should put on the inner cover, but I didn't, being unsure of how I could then look into the hive.
The two frames I had put into the top super still had brood in them, or maybe new brood; no honey. I took two more frames with some brood from the middle super and switched them with two frames from the top super. According to Franklin Carrier, this is done to prevent swarming and to make more honey.
I spotted the queen in the middle super. When I moved the super, I, again, placed it very carefully on the top super which was on the inverted lid. (Moving these is a bit like the Towers of Hanoi.) I noted which frame she was on (4th) and when I put the super back on, looked to see if she was still there- she wasn't. I looked at the two frames to either side- she wasn't there either. I then put the top super back on and looked there for her- no luck. I looked all around the ground and didn't see her or any other bees. I can only assume/hope that she just moved to another frame or into the lower brood box.
Before going into the hive, I prepared the drone brood frame. I uncapped the cells with a fork. Many of the dead larvae had liquified. So, naturally, I wondered if this was because of foul brood disease. Larva that die from this do liquify. But, I figured that it is unlikely that my hive is infected. There should be evidence of disease if it were there and these larvae had been in the freezer for 2 days.
On a more interesting note- I started reading The Biology of the Honey Bee by Mark L. Winston, one of the textbooks that was recommended by Thomas Seeley. I've learned some fascinating stuff. Bees have sensory hairs between facets of their compound eyes that sense wind direction. This allows them to adjust for wind-drift when trying to fly in a certain direction. They can sense which direction odors come from via their antennae, there are special notches in their forelegs they use to clean their antennae and there is an intricate arrangement of hairs and bristles on their hind legs that is used to pack and carry pollen.