Killed a bunch of brood.

I took the U of M Short Course several years ago, and only within the past couple years came to understand how those three deep bodies are actually supposed to be used, in part because Gary has updated the way he explains it. I might not be able to do as well, but here goes...

Going into winter, the goal is to have the top and middle boxes more or less full of honey and pollen. The bottom box may actually be empty once the queen finishes laying eggs for the year, and that's OK. The ultimate reason you're rotating boxes is not to determine the shape or size of the brood nest, but to take advantage of the bees' behavior to ensure that the pollen is distributed throughout the top two boxes when you go into winter. This way they can reach pollen stores to feed the earliest brood when it's still cold (and potentially very cold) in spring. There are several bee behavior patterns that make this system work. Bees will store honey in the top of the hive; this works because the field bees pass nectar to house bees when they arrive, and the house bees carry it up. Bees store pollen closer to the door, because the field bees carry that to the cells themselves. Thus your top box will tend to accumulate honey but the pollen will accumulate lower down, closer to the current brood nest. Italian bees will also try to put the brood nest as high up in the hives as they can. That means that as the nest shrinks in fall, they will likely stop using the bottom-most box altogether. It also means that when they start up again in spring, they'll be raising brood in the top box using cells that they ate the honey out of over winter. Because it spent some time near the bottom of the stack the year before, that top box will also contain some cells of stored pollen, saving the early spring nurse bees a long, cold, potentially deadly trip down to last year's brood nest in the lower box.

My first couple years, I misunderstood the system and tried to rotate boxes to get them all full of brood, then all full of honey. The brood nests never grew to 3 boxes worth, but I did get them to pack all 3 with honey a couple times and that was a disaster. Don't do it that way.

Mites are attracted to drone brood. If you look carefully in the future, you may spot a mite or two inside one of the drone cells you break open when doing inspections.

I've found that since I started adding at least one foundationless frame to each colony to allow the bees to produce drones, they build much less drone comb between the boxes. This saves me having to decide whether to spend time scraping it off or squish bees when I put the boxes back together. Once you really become a hardened killer, you can use this technique to reduce your mite population by pulling that drone frame when it's capped, and sticking it in the freezer. This will allow you to practice your heartlessness for next year, when you'll have to kill off your entire first colony if you continue to follow the U of M system.

Thank you for the good pictures and information in your blog. I think other beginning beekeepers are likely to find it helpful for understanding what they might encounter.

I was touched when I saw the nurse bees busy around my broken drone comb too, until they had had a few minutes to work on it and it became apparent what they were actually doing. It's much less tender than it is deliberate.

If there's already honey in a cell, the queen can't use it for brood. In the recent good honey flow, your worker bees went looking for empty cells to store nectar in and found them in that top super, before the queen got there with her eggs. She can probably find plenty of room in the lower two boxes for brood. Your goal is to get a few pollen cells mixed in with the honey before winter. It might be possible to arrange for that by moving the boxes around, but if it doesn't work you can always move frames from box to box in fall.

plaztikjezuz: I guess gophers do too, though it may be less common.

S. P., please take my suggestions with a grain of salt. You need to get to the point to where you are not micro-managing your bees. This is a very common mistake of new beekeepers who are truly trying to care for their bees. If you don't lighten up and let bees be bees you are going to burn out/throw your hands up and quit.
I can't speak for your geographical region but in mine there is no reason at this time to be reversing hive bodies, the season is basicly over. Swarming season is over, if they did swarm at this time and successfully raise a new queen you would just have a younger more vibrant queen in the spring.
Think about the drone brood you scraped off. If they want it they will just build more, no need in scraping it off. They also use it as a "ladder" from one box up to another.
Bees have survived for thousands of years without our help. If you don't have a definate, sound reason to go in a hive why do it?
I'm not advocating neglect, just sound management.
Relax and enjoy your bees, see how much you can disern by just watching their behavior at the landing board.