Hi Curt, from what you wrote you put all the old comb into the medium super right? If so, put the medium on the bottom board, drill a 1" hole in the deep between the hand hold and the bottom of the frames (regulate the holes size w/ a cut up cork), wait till the queen moves up to the deep (you'll start finding eggs in the deep). Put a queen excluder between the super and the deep just to be sure (or find the queen in the deep). After a couple weeks you should have pretty much all the brood hatched out and you can start carving on and or culling the old comb.
I did a couple cut outs last year and I know what you mean about feeling like you're tormenting the bees, but you want to get that old comb culled out.
I did a couple cut outs last year and I know what you mean about feeling like you're tormenting the bees, but you want to get that old comb culled out.