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Two queens?

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I'm a relatively new beekeeper (third summer, but first year had a rough learning curve). Both hives overwintered well in two deeps this past year. One of them (Thing 1) came out of winter incredibly strong and built out ~3 medium supers from foundation, on top of the two deeps and a queen excluder. It made swarm cells, but I split out one of the deeps into two nucs with some of the cells, added back a second deep of foundation, and it never swarmed.

Last weekend (6/8), I saw open brood in one of the deeps of Thing 1 which now had 4 supers on top and an upper entrance. Friday morning (6/14) I put an escape board on that hive and another on my second hive (Thing 2, with 3 supers, closing the upper entrances of course). Saturday morning (6/15), Thing 2's supers were pretty clear. Thing 1's were not at all, and the reason was apparent when I found 12 of the 40 "super" frames with brood. My eyes aren't good enough to see eggs, but there was clearly capped brood in a great laying pattern and open brood around it.

I figured that on 6/8, I must have accidentally knocked the queen into the honey supers when I was looking through the deeps. So, I took the hive apart, removed the queen excluder, consolidated the "super" brood into two medium boxes and got ready to put them on the deeps directly. I decided to look at the deeps and was flummoxed to find tons of beautiful capped brood, plus a bunch of fat open brood, at basically the same stage as the ones above the queen excluder. Sorry for the long description, but what is going on here:

1) Two queens laying in one hive, one above and one below where the queen excluder was?
2) A queen who can move across the queen excluder?

Right now, the arrangement is two deeps, two mediums with lots of brood in the bottom box and two frames with brood in the top box (rest foundation to discourage the queen from hanging out there), escape board, two medium supers with no brood. I had planned to see if the top two mediums were cleared tomorrow, and if so, replace the escape board with a queen excluder. I would then work the queen down as brood emerged over time.

Is my plan okay or should I do something else?

Thanks.
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