Karen,
I don't open the brood nest it stays together in one brood box and is placed in the bottom position, the 2nd and 3rd deeps are checkerboarded above the nest. The temperature swings don't concern me since the population is large enough at this time to keep the brood warm, however there are times of extreem cold when I see a few white pupae being removed from a hive but it only amounts to a few that got chilled at the outer edge of the nest.
I consolidate the hives into a 2 deep configuration for winter, any hives needing stores in their second deeps is supplied from the frames in the third deeps then I extract the rest of the third deep frames. After extraction I stack these third deeps outside for a day and let all the bees have a hay day picking them clean. These third deeps are then placed back on the hives either above the inner cover or on the bottom of the stack in first box position, and stored there all winter. Any pollen or capped honey left in them isn't a problem, it's no different than any of the other honey or pollen in the hive.
The third deeps are on the hives year around to keep the wax moths out of them, the bees take better care of the comb than I can. During spring and summer they are in use and during fall and winter they are being stored.
If I can be of more help let me know.....Bill
