So, I have questions:
What's going on above the excluder? Sometimes your queen excluder will become a "honey excluder" if the workers don't like to pass through it. If nothing is happening above, maybe take the excluder out. You can always put it back later. It certainly sounds like you don't need it now.
How many deep boxes are you using? (1 or 2); and -
Where are these full of honey frames located in the box? If the cluster is significantly smaller than the available brood chamber, they may just fill excess comb with food stores. If these honey-bound frames are from the sides of the box, I would leave them be.
How is the queen doing with the space she is using? Good laying pattern, lots of bees, no signs of swarming? tell us more.