I am surely no expert but did you inspect the supercedure cells you left was one open and the other damaged. Could the third queen have been out on her mating flight. the first swarm was the old queen and the second one being the first emerged queen. Id check back in a few days and see if there are newly laid eggs, Although you did say there was a new supercedure cell so it is probably a good bet that the hive was queenless. I think Id want the old queens genetics and let the new queen emerge and mate. If there is still an abundance of nurse bees on the brood you can always make a nuc out of her and place the bought queen in the hive. Just my opinion though.