I have two hives that I have been moving toward using mediums. The queens are up in the medium with a queen excluder between the deep and medium. The old deep super has duragilt foundation which I don't want to continue with.

1. How do I decommission the old deep? After any brood in them hatch out, will the bees fill the comb back up with honey/stores?
2. Should I cut the duragilt to medium frame size and keep any honey stores for this winter? Both of these are from spring swarms caught this spring. I am heading toward foundationless....already using in the mediums.
3. I have a new top entrance (shimmed migratory top) but I have been hesitant to close off the lower entrance (half-open). So the bees are all going in the bottom through the old brood super, up through the excluder, to get to the mediums. Is it harmful to close off the bottom entrance? Should I leave a small (3/8") opening in the lower for any drones?
4. It seems if I can get the bees to use the upper entrance I will have a lot fewer bees in the old deep..is that so?
Do I shake/brush the bees off the frames of the deep when doing the removal or do I use some kind of bee escape?

Thanks, Jim