Cups don't count, the girls build them out all the time, it's the cells that count. With only three cells found, I'd say it was supercedure. I'd say you have a nice virgin queen in the single story hive and you've got a caged queen in the 2 story hive. You might have another queen in the 2 story hive as well though, so check on the caged queen to see how the bees are treating her.
With all the honey found in the hive, it is also possible they had already swarmed of course, but I think you'd have found lots more queen cells throughout the hive in that case.
With all the honey found in the hive, it is also possible they had already swarmed of course, but I think you'd have found lots more queen cells throughout the hive in that case.
