Ok I am starting my second year. I have a colony that someone gave me last year that was a 1 year old swarm in 2 supers with frames no foundation. They built wacky comb. I tried to cut the comb out and rubber band it into medium frames but my mentor got worried we were damaging too much brood. So I put a hive body on top of the two supers with the swarm hoping they would move up last year. On top of that I put a medium in case they did with a few frames of brood rubber banded. So the current configuration is super, super, deep, med, impre shim , inner cover. Well they did not move up last year but produced me 7 gallons of honey. They have always been a huge colony and productive. 2 weeks ago I got into them and the medium which is on top was full of bees and honey, the deep above the 2 supers and below the medium was a brood chamber and every frame had brood. They were starting to lay brood on the burr comb between the medium and the deep So I felt that I needed to reverse the deep and put it on the bottom the first chance I got. So today I went to do that and opened it up and it was jam packed full of bees and they were laying brood and making comb on top of the frames and to the inner cover( I also had an impre shim below the inner cover to put on sugar patties). I think now I got brood chamber from the deep all the way up. They must have built the comb under the inner cover because they have no room from the deep up. I have not been able to get into the bottom two supers to see the situation. I suspect it is empty. I took the medium off and they had brood in the burr comb between the medium and the deep. I lost my nerve and buttoned it all back up. So what do I do from here. I had planned to split this hive at least once maybe twice when the weather got to where it did not get into the 30's at night.