I am new to beekeeping and happy to join this forum. My new bees adapted well and the colony grew pretty fast throughout the spring. I spotted my queen only once but was pretty happy she was laying since I had a healthy number of capped brood and larvae. Once 80% of the frames were populated I decided to install my super. However, I noticed at least 5 queen cells. At first the colony was pretty busy on the supers, not impressive activity but I could see a good number of bees waxing away. I explored the hive today only to find the super quite empty. I inspected the brood box and still could not find the queen. Some of the queen cells were open and the number of bees seemed a bit lower. I suspect they swarmed without me noticing. I was also surprised at the amount of drones!!! We have a short pollinating season in the north east of the USA and I am puzzled about what to do with the super. Should I take it off? Will it be hard for them to heat and patrol in the winter now that I think a swarming event has decreased my bee numbers? Since I still have queen cells could they swarm again?
Hi and welcome to the forum. Yes, take the super off and store it somewhere dry and protected from pests. And yes, it does sound like your colony has swarmed - and yes, it could swarm again. The large number of drones could be a normal result of the population reaching its peak just prior to queen cells being built, or could be because you have a laying worker - which happens when a hive has been queenless for too long. I think it’s more likely that a new queen is out on mating flights and will soon return and begin to lay, and the drone to worker ratio will go back to normal.
However, without having a better idea of the sequence of your observations, it’s impossible to tell whether your colony has swarmed only once, or if it may swarm again. I strongly suggest you try to get an experienced local beek over to inspect with you, so you can take the right actions to help it stabilize.
Don’t worry too much about the smaller colony size - loads of people successfully overwinter single deeps and even nucleus boxes. The key is to prepare well in advance of cold weather by treating for mites, ensuring enough food stores, and insulating.
Lastly, give the search feature a try and you can delve into the previous discussions on all the issues you mentioned.
Good luck and let us know how it goes 
Thanks so much for your response Eva! My mentor is out and will return next month. Hence I’m currently operating under the premise of bees do what they do and nature is savvy! There is still ton of activity at the hive which reassures me. I’ll remove the flow super and store it. I’m prepared for the fall mite treatment and insulation as well as feed.
Thanks again and will keep you posted
Wouldn’t hurt to do some oxalic acid before there is capped brood again but make sure you wait until you’re sure you have a laying and well accepted queen.
Yes, thanks. I m still trying to figure it out. And I do have capped brood. I guess this coming week is key.
You were right @Eva @chau06 !!!
I walked to the hive this morning and there she was. I guess back from a mating flight.
She is gorgeous. A tad smaller than the queen before her. She has a beautiful reddish color and has a lovely torpedo like body. No black stripes.
I softly saluted her majesty!!! While she “clumsily” flew back inside chaperoned by a few others.
Here is her photo
Her royal highness:
And here is the entrance of the flow hive with a worker to contrast:
Can’t wait to check on her progress, inspect the brood, and search for eggs and larvae. I’m sooo hooked.
Thanks again for your amazing support!!
You may find that she gets longer and bigger once she gets her egg laying on in earnest.