I did that last week after noticing the babies had pretty much hatched out of the bottom box and that it was the top box that had swarm cells, presumably because Queen Elizabeth was feeling crowded. Putting the now mostly empty bottom box up top gave her wiggle room. And since the queen seems to prefer to move upwards to lay eggs, she had a whole new box!
Strangely, I also put an entirely new box of frames with empty foundation on the very top of it all but the bees have drawn no comb at all in that - why not??