Two queens, Dilemma

[Cestria]

I have one hive that came through last winter very strong so I was hopeful of a productive year, however my bees have kept me on my toes and I now find that I’m in a predicament.
During the early spring I was doing regular inspections all seemed well, the hive numbers were increasing well I even spotted her majesty, there was no signs of disease and plenty of stores were seen.
At the end of May there was a cold snap so I missed a regular inspection, thinking it was best to leave them alone whilst it was cold. The following weekend I was due to go up to the hive when I had a call from a neighbour letting me know the bees had swarmed. I must have missed the queen cup on my last visit and because I missed a week they’d capped it and were off. When I got to the apiary the bees were still on the wing but I saw them starting to settle in a nearby elder tree. I decided to let them cluster and aimed to return later that day to try capture the cast. Sadly when I got there they had gone.
I left my hive in peace for a couple of weeks before doing another inspection to let the new queen emerge and have her mating flight. When I did my next inspection I lifted off the super which was still very heavy and went straight to the brood box to my dismay when went in there was no sign of brood and the frames when to all intents and purposes empty.
At this point I decided, to give the hive a chance of survival I would re-queen with a mated queen I would buy from ******.
After two weeks I’ve gone in to find that the new queen is laying strongly with good signs of brood and eggs.
The problem is that for the first time since the swarm have closely inspected the super frames and I have found that there is a quantity of brood on the super frames.
So I’m now trying to work out my plan of attack
My first thought is to find my bought queen, she is marked and should be easier to find, take her with some of her brood frames and start a neuc with them. Remove the queen excluder top let the ‘top’ queen go down into the brood chamber then try to get both through the winter.
My second thought is to try to find the ‘top’ queen to destroy her, let the brood that is in the supers emerge then get the single stronger hive through the winter.
The third thought is to follow any sage advice I can get

 

[parkranger]

Are you sure that you have two Queens and not just one Queen passing the excluder?

 

[Travelator]

Think about your long term goals first and then decide what to do. Don't let events overtake you.

Do you want to get up to two colonies and have a better chance of at least one surviving the winter (but not much chance of any honey this year)?

Or would you prefer to aim for some honey and go into the winter with a single colony?

 

[Arfermo]

I don't advise destroying any queens until you are sure what is going on. The first question to sort out is whether there is brood above as well as below the QE. You suggest not. In that case, surely all you need to do is shake all the bees into the bottom box, brushing any off any super frames (I use a soft wallpapering brush to handle the non-flyers), stick the QE back on and hope the Q is not so skinny she can get through the QE. After that, see how it goes for a while without panicking. The brood in the supers is not a problem if you can ensure the Q is where you expect her to be.

 

[enrico]

Or......take the supers off and put them on a new floor with a roof, and new supers on the Old hive. You now in theory have two hives. If you get eggs in the super on the old hive again the QE is crap. If you get emergency cells in the hive with the eggs then there is no queen in there, either way you now have two hives instead of one which is always a good thing.
E

 

[Finman]

.
Take excluder off. If you have 2 quees, slower one will be killed.

Then put the excluder again. If the hive needs it?