confused by queen activity

[brolib]

Greetings,
I'm really new at beekeeping. Got a couple of hives and packages late April of this year and everything seemed to be going along smoothly. One hive appeared a bit weaker than the other so the stronger hive "donated" a frame of brood to the weaker, then added another deep body on both hives. That was 4-5 days ago. Looked in on them this afternoon and there was a small "beard" of bees hanging down from the entrance. I looked through the hanging bees and didn't see a queen. Removed the outer and inner cover to check for drawn comb. There was hardly any. Thought I'd give the bees on the inner a cover a quick look and there was a queen! I grabbed an empty hive I got in case a swarm needed a home and placed it upwind about 10 feet with some lemon grass oil inside hoping to attract a swarm leaving the hive.
What in the world was a queen doing at the top of a deep super that has no comb? Should I capture her and put her in the new hive along with some brood, assuming that she's a supercedure queen? I've never seen half this much traffic at the entrance of this hive. Any ideas on what's going on would be appreciated.

[GSF]

They may be fixing to go look for another place. They say packages will do that some times. Is this one of them that has a frame of brood donated to them?
If not then you may want to donate one as an anchor. Could be that the queen isn't mated.