Not sure what is happening. I've scoured the forums looking for answers but nothing conclusive. Please help.

Here's what I've encountered in the last couple weeks

about two weeks ago I inspected the hive (Warre hive). Everything looked good. top box full of honey, middle box almost full of honey/brood, 3rd box empty, but comb is making an appearance. Bees are working hard, not too many hive beetles.
past two weeks: Very hot/humid in the day, very rainy at night. Lots and lots of bearding. It scared me at first but then i read about bearding and felt fine about it. It was fun to watch.
tropical storms picked up and we saw some flooding. My wife woke me up at 4 a.m. to tell me she "thinks the bees are under water." I took a look but didn't see the water level as a threat but when I woke up, there was a water-line above the hive entrance.
feeling terrible, i added some height to their foundation.
One day lots of bearding around 5 p.m. almost the entire front-side of the hive covered in bees, went to look at them again around 6:30, they were gone. Hopefully went back in, but did they? the temperature did not drop much if at all. Why would they go back in? did they swarm?
At that time i noticed some poop smears on the hive (see pic below).

Got freaked out. I know they are stressed. Decided that they were probably out of room and would add a box as soon as weather permitted.
A couple days later, as soon as the weather was right, I went in the hive: top box, unchanged, middle box, empty, dark comb. A few capped brood cells at the bottom, which is where we saw workers pulling pupae out of their cells. The pupae isn't chalky, or scaly, or brown, it was just soft and white. Up-close they looked like healthy brood. (but what do I know). We pulled the bottom box off and saw A LOT of dead pupae and larvae on the hive floor. (See pictures).

So i wonder: What is going on? What do I do? What did I do? Anything I can do?

Any advice would help. Thanks!