I would cut one or two of the deep brood combs to fit mediums and tie them in. Then confine the queen with those. Otherwise, I have seen a queen abandoned when doing what you propose.
hmm...actually you know I should of thought of it a bit more before answering. you of course are right, putting a queen into a empty medium and just expecting them to leave the brood and follow her up and start anew can have problems. thanks for the catch on my semi-bad advice. I was probably thrown off trying to decipher specifically what he meant. I'd keep the deep personally and just put the medium on top, then after the medium is stable and solid, maybe even next spring rotate the deep out, if I wanted. (I'd actually still keep the deep but I like deeps and jumbo's compared to mediums for brood. I like having more space for them to move in the micro climate before crossing a box boundary I guess and more space for laying on a frame. and natural hives are often way longer.)