Sounds to me like you were too late putting on the second box, and your original queen swarmed, capped brood emerging was enough to make it so that you didn't notice that there were bees gone.
As far as where the next queen was when you looked, you'll have to do the math- it takes 16 days from egg to new queen emergence, then it takes some more time for her to get mated and start laying. If she was successful, you should start seeing the signs not too long from now.
As far as where the next queen was when you looked, you'll have to do the math- it takes 16 days from egg to new queen emergence, then it takes some more time for her to get mated and start laying. If she was successful, you should start seeing the signs not too long from now.