Koopa:
Yes, if they're in the top box and the bottom box is empty, just take that box off completely and let box #2 become the new #1, then you can put fresh foundation in a box above that. I would definitely keep the crazy messed up comb however, because it would be very useful for swarm traps.
Deborah:
At the very least I would burn the frames and then wash the box down with a bleach solution. I don't think its overly likely that its all infected with anything, but better safe than sorry.