Yes, I plan on continuing this year. Yes, there is plenty of honey in hive #2. I treated with a menthol patty in both hives. I did not make the patty myself, they were given to me by a coworker who keeps bees (actually, he lost 5 out of 7 hives last year, so maybe his "treatment" is/was faulty?).
So, I can simply leave the deep super in place and plan on using it with the new bees this spring. If it was tracheal mites, what do I do with the contents of the brood chamber, exactly?