I am guessing that the queen moved up, and that the bees followed her?
Maybe yes and maybe no. The queen doesn't have to move up for the bees to occupy the upper super. By removing the excluder, you just gave them easier access to occupy it. Lets face it, if you had to twist, contort, and squeeze yourself thru the doorway to get into one of the rooms in your house, you would spend a lot less time in that room.