Mostly you need to keep in mind that pulling honey is a normal part of beekeeping. Pulling brood is not. So what you want to do is get the brood nest in the mediums so at harvest time you can pull the deeps. If you put a medium frame in the center of the brood nest (when they can handle it which, in MO, I'm guessing will be about April) you can pull that frame of brood up to a medium box along with the queen above an excluder and soon you'll have a brood nest in the medium instead of the deep. You can just add medium boxes as usual on top until harvest time when you will take the deep off. You might check to make sure they don't rear another queen in the deep.
If so I'd move her up as well.
The "brute force" method is to do a cutout (cut the comb out of the deeps and tie the brood into medium frames). But this isn't really necessary unless you are impatient.