The queen won't have had much of a chance to lay very many frames, so find the frames that have been laid in, put them in one box, take away everything else and set a deep on top of the honey super w/ the eggs in it. The queen will move up into the deep after a while and you can then remove the honey super from underneath.
When you say that these are not mediums but honey supers, does that mean that they are shallow supers?
You could take everything off of the bottom board, place a deep there, shake each frame of bees out of the honey supers, find the frames that the queen has laid in, place an excluder on the deep and set the honey super w/ the frames w/ eggs on top of the excluder. After some time the eggs will mature and emerge and you will have a honey super again.