I suspect this is going to be a loooong process. Even if you get the queen out, the old comb will still be under there and act like a great swarm trap.
So, to continue your process, the bees appear to be cleaning and if the queen runs out of room below she may move up. You would need to find her in that box and put a queen excluded under it thereby trapping here in the deep. After a three weeks, the brood below will have emerged. You could then try heavy smoke and carefully placed Honey-B-Gone to encourage all of the bees below to move up. Finally, you would move the deep onto a bottom board into it's new location. The foragers will go back and clean up what they want from the old location. I think this would be called a wishful thinking, encourage out (TM).
I would probably look at lifting the entire deck and cut them out from below. Depending on how it is anchored, that may not be possible. If not, I would suggest cutting the boards near the joists, removing the bees and comb, installing sleeper joists, and putting the boards back down. I've done sheds both ways.