I have three deep supers full of dead bees and mold. Should I clean them and pull all the dead bees and wash off the mold or will the new bees just clean it up like new or almost new?
I'd give the woodenware some TLC, particularly I'd try to scrub off as much mold as possible. I don't think it will ever completely go away, though.
If there's someone available to hot-wax dip those boxes, I'd definitely go that route.
The bees will clean it up if you give it to a strong hive.