I inspected this hive today, and I think it was just some sort of swarm/supersedure weirdness. The population bounced back significantly this week, and there was some brood in the bottom box again. I only saw one queen still, and I was keeping an eye out even after I saw her. My more careful eye this week also found two very small hatched queen cells. I probably thought they were cups before, honestly I probably didn't see the one at all since it was below some drone brood, but upon closer inspection today I noticed that their edges were ragged like they'd been chewed, not smooth like an unused cup. There were far less hairless bees today, and the weird smell wasn't there either (perhaps that was just a fluke). Thanks so much for all the help guys, I was worried about them last week, but it seems like it was nothing, just an odd-looking queen changeover.