Helping my mentor out a little over a month ago during late winter or early spring, is when he actually reduced a few hives down to one box. Typically they will slowly move up to the top box and likely all you need to do is remove the bottom box. Occasionally there will be some honey left in the bottom box where you’ll need to make a decision on whether to move those frames to the box you’re keeping or possibly just lay the frames outside in front of the entrance so the bees can remove what they want.
Yes you’ll just have to make sure the Queen is transferred or in the correct box. This may entail taking your brush and sweeping all B’s off of each frame into the box or keeping so that you can ensure she is in the right box but make sure you don’t sweep hard enough to hurt her. You could just give it a good bang and the all drop into the correct box.
I additionally thought this posting was great
http://forum.honeyflow.com/t/bees-not-using-the-flow-frames/6318/2?u=martydallas