Wondering what he Best course of action when brood is found in the hone super. Suspect the queen is in th brood box currently. 3 out of the 6 flow hive frames have some capped brood. 1 in particular has at least 50%.
Any advice would be appreciated.
What I generally do is make sure that there is no gap in the QX after shaking all of the bees into the brood box. Normally I’ll find worker brood in the honey super. In your case you’ll need to check if there is any worker brood in the brood box. You need to determine whether you still have a queen or a laying worker.
My course of action is somewhat controversial, however what I would do, provided the colony is strong with workers is fracture all of the caps on one frame, then replace all of the frames. The workers will remove the damaged brood & then clean the frame up ready to fill with honey. Do the second frame in 2 days time, provided the first frame is successfully cleaned up. Then the third frame 2 days after that.
This is all provided that you found the queen & have her secure in the brood box.
Then there is the issue of the leftover cocoons. I would leave them there & see what happens.
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Do you have a rationale as to why the queen was in the honey super? Did you use an excluder or is it damaged? Did you checker board and left bees on frames moved up? Curious to understand the underlying reason as well as working through the suggestions to fix. On the clean out side there is a couple of YouTube videos that show this and how it was managed as well as the Flow video on disassembly and assembly.
good luck.
Adam
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Hi Danica,
Looks like you have drone brood in your Flow. Have a look at the following FAQ for guidance.
https://www.honeyflow.com/faqs/all/what-would-you-do-if-you-got-drone-brood-in-the-flow-frames/p/117
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THanks everyone for the advice. We do have a queen excluder in place and don’t seem to have any gaps. Will remove the queen excluder and possibly add an additional brood box and replace excluder on top after carefully shaking all bees down a level and checking for the queen. Will check on the lower brood in the process. It was originally a wild hive but we think it was from another swarming hive as they are very calm bees and never had an issue with the queen. The brood box at the bottom is however a natural formation and challenging to check all the frames as they are quite knitted together with combe.
Not sure as to how she has moved up. Will have a closer inspection this afternoon or tomorrow when the weather is better again as very windy now. We have a queen excluder in place and no apparent damage, and brood was healthy on last inspection a few months ago. We did have a wet winter and was worried some moisture got inside the top. They have been super busy in the last month and almost filled all the frames with honey up top, so now also need to make sure there is enough room for them all, or wether to add another brood box while inspecting it all
Danica,
You got lots of great ideas n thots to work with so I’m not adding … Don’t panic ! Queen upstairs happens to all of us sooner or later…
I work with a small commercial beekeeper. We had brood in the honey supers twice this last season. My personal Apiary I’ve NOT yet ! But it will happen sooner or later.
Do your checks n choose your path from the advice given. If you have all staged brood below too … just really check for the Queen n get her Buns below. If laying worker … do confirm you have a Queen (all stages of brood down to those tiny hard to see eggs (my eyes 
suck so I have to wait for first day larva to see)…
Good luck 
,
Gerald
Hi Gerald
We were finally able to inspect our hive again and not sure it’s good news. Looks like we have honey in the brood box, and as we had a wild hive and used their comb, nothing is neat in the brood box and all woven together with comb and very difficult to cut apart without causing damage and huge distress. We managed to inspect a few but couldn’t see a queen and suspect she was at the top.
We inspected all the top frames but due to so many bees was difficult to see a queen. We shook and transferd as many bees into the brood box, and think there was a queen in there as the bees were clumped around as if to protect her. We put the excluder back in place and all the flow hive frames back up the top (3 of which still contain brood which look like they may hatch soon, but didn’t see a queen cell). Not sure if we just leave them there, or replace the frames. Someone also mentioned rupturing them, but not sure.
Any ideas?
Will check top again in a few days and make sure there is not more brood up in the top and see if the brood has hatched.
You could leave them to hatch out- given there may be eggs in there- it could take as long as 21 days for them to all hatch. Also that assumes the queen isn’t up there- or doesn’t return.
Ideally you will have to deal with the brood box also. One long-term low disturbance option could be to add another brood box under the original- with all wired foundation frames- wait until it is fully built up (2 months?) then move the QX to below the original brood (making sure the queen is in the new bottom box) so that everything can hatch out if the old brood box. Once that’s done they should fill it with honey- and then you can harvest that completely- cutting out all the combs to start over fresh …
So the plan could be:
let the flow super hatch out- then fill with honey until autumn. You could take it off before winter to harvest and to fully clean out the caccoons… you could leave the old wonky brood box on top of the new clean brood box- with QX between -over winter. Next spring take off the old brood box (harvest whatever honey is in it)- add the cleaned flow super back- and maybe just maybe all will be good!
What type of QX are you using? Be good to find out how the queen got upstairs in the first place as this plan will require keeping her below the QX at all times…
Drones=26 days to hatch
Workers 21
Queens 16
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Nope. They all take 3 days to hatch. Eggs hatch. Pupae emerge… 
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As Jack @Semaphore suggested, it would probably be best to let the brood emerge first, now that you have got the queen back down. If she doesn’t get past the QX again, and the brood is all gone, I would actually suggest trying to borrow a spinner from somebody. You could scratch the cappings off the honey and spin the frames gently to get the honey out. I would not try to use the Flow mechanism, because the cocoons from the brood will probably make most of it leak out of the frame. Plus the honey will be contaminated with larval poo. If you spin the frames, that won’t happen.
Then you will probably need to dismantle the frame to get the cocoons out. You might be able to do it by hand with a pair of tweezers, but given the amount of brood in your photos, I think I would just take the frames apart and wash in warm soapy water. Flow has made some good youtube videos on how to do this, and I think in the end it would probably be the quickest way to clean up.
Please let us know what you decide to do and how it goes. 
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Hi Danica, my priority would be to get that brood box in good order so that each frame can be readily inspected.
The options with the drone brood are #1. as I described, the worker bees will tear all of the damaged brood out of the cells, through the QX, then out the entrance. The ants will get a good feed. #2 Let the brood emerge above the QX, that will take a lot longer to happen. You will need to provide an exit for the drones, otherwise they will get stuck & die trying to fit through the QX, clogging it up in the meantime. SHB is another issue. If SHB are in your area, those dead & dying drones stuck in the QX are a magnet for beetles to lay eggs in.
My mentor/life coach, (SWMBO) says that she has no problem with honey out of comb that has been cracked after brood has been raised in it. I agree. 
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ah- semantics… I’m going to stick to hatch. It may be technically wrong- but poetically it is just right.
Thanks for all the advice guys. So have opened the hive again and inspected each of the top flow frames again. The 3 that had brood are now mostly hatched. They also seem to have cleaned up most of the cocoons. This is what it looks like now.
Looks like we got the queen down
Stairs as they have now moved a lot of honey from the bottom to the top by the looks as the frame we inspected with honey in brood box is now empty and the top flow frames that we had previously emptied 2 are now almost full again and only been 10 days or so.
Have tried to shake and sweep as many bees from he top back to the brood box below the excluder as there were a lot of drones. Will check again in a few days to make sure they all go down and hatched.
That’s good news!
did you see fresh eggs and/or larvae down below in the brood box? If not you may want to check to make sure you have a laying queen down there? Also did you ever work out how she got upstairs?
Once you’ve confirmed that- do you plan to remove the flow frames- empty them- clean them and replace?
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Make sure to provide a top exit so those hatching drones can get out of the hive.
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Hi Danica, It is unlikely that the bees will remove the cocoons. You should remove the Flow frames and clean out the cocoons before allowing the bees to put honey in those cells as you may not be able to harvest the honey from the Flow frames otherwise. Those cocoons will block the flow of honey to the bottom channel. Its better to be sure and clean them out now rather than wasting all that precious honey.
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It would be interesting to see what happens if those cocoons weren’t removed. Because they are VERY thin, plus they tear easy. It could be a lot of work for nothing. I think I’d take an each way bet. Clean some & leave some as a kind of experiment.
I brought some frames home to extract today. A couple of frames have small amounts of drone brood in them. Sometimes a worker will decide to lay a few drones above the QX. I guess that’s why it’s always best to check the flow frames before harvest.
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