I really messed up this time. two weeks ago I went into the hives and I left the queen excluder off one of them without realizing it till now. Can’t find the queen so that means I have not a clue as to what to do from here. Don’t ask me how I did such a dumb thing. Oh…yes she has been laying in the flow frames.
Hi Chet, I’ll start the responses by saying that I would probably take the lid and cover off the flow super and smoke as many bees as I could down into the brood or supers below. Then I would take the flow frames out one at a time looking for the queen. If you can’t see her, shake the bees off as best as possible down into the flow super box and check again for the queen. If she is not there put the flow frame carefully to one side. Repeat for the remaining flow frames continuing to smoke them as necessary. When you end up with all the flow frames as clear as you can of bees check them again for the queen. If all is clear take the flow super off. Clear the bees off the top of the box that was/is below the flow super and put the excluder on. Then add the flow super back on with the frames back in it. I’m not experienced with eggs etc above the excluder but I understand they will be ok and the bees will deal with them fine. Let’s wait and see what others think!
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Lots of people do that deliberately, so don’t beat yourself up too much! 
My queens are all marked, and half the time, I can’t find them either. But I have to admit I don’t spend much time looking for them. If the hive is happy and I see BIAS (brood in all stages), I really don’t care too much about putting out an APB (police-style) on the queen.
Now in your case, somebody has been laying in the Flow frames - probably your queen, but she may not be the only culprit. I would put in the queen excluder now, having smoked down from the top. If you still see eggs and uncapped larvae next week, try to take some pictures. If the eggs are singles, the queen is still above the excluder. If they are multiples and off-center, you have laying workers and we need some different advice. 
Meanwhile, if the larvae in the Flow frames are uncapped, you can freeze them for 48 hours, then replace them, to get the bees to clean up and save you some work. 
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I should have said larvae , some are far along too. thanks to both of you for your help.
I have quite a bit of both capped and larvae. I am just guessing but don’t think it’s laying workers so I guess the most pressing problem now is the capped brood in the flow frames. If I just brush off all the bees and put the excluder on, will the capped brood problem just go away when the capped brood becomes bees? This same hive is busting at the seams and I have a more experienced helper tomorrow and we will try to do something even if it is wrong.
Errrrmm not really. You will have 2 new problems. First, most of the bees hatching will probably be drones, and unless you make an upper entrance, they will be trapped above the queen excluder. Second, they will leave behind cocoons, which will probably disrupt the flow of any honey when you try to harvest later in the season.
If it was my hive, I would probably smoke the bees down, then put a traditional medium super on below the Flow super and above the queen excluder. I would let the larvae hatch, and use my inner cover which has an upper entrance to let the drones out. In 2 weeks’ time, if there are no new larvae above the queen excluder, I would remove the Flow super and clean out all of the cocoons.
The reason for the extra medium (or shallow or even deep if you have one) super is twofold. First, if it has wax comb in it, the queen will preferentially lay in that if she is still above the QX, especially if you put it below the Flow super. This will stop your Flow larval problem from getting too much worse. Second, if your existing brood boxes are overflowing with bees, they will have something to fill while you let the flow larvae hatch and clean up the frames.
Please post what you you decided to do. You are not alone, and a lot of people can learn from you!
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Rather than trying to smoke them down- couldn’t Chet take the flow super off and one by one shake the flow frame bees off onto the brood box?
For sure, but I hate shaking queens.
Yes shaking the bees into the brood box is a good idea. I would check each frame before shaking in case you see her, if you do, simply nudge her onto the brood frames. After that you wont need to shake any more bees. Make sure you have an exit for the drones after they hatch. Otherwise they’ll die trying to get through the QX, that will be a magnet for SHB to lay eggs in.
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I do have an upper entrance they are using already. we will get back to it around 3 today and I will try to make a good vid. I am still conflicted about what to do on the capped brood in the flow frames.
It’s easy to find her if she’s up there. Remove the Flow Box, install excluder onto brood box and place an empty super of any size on top of that. Gently shake each frame onto the excluder. Smoke the bees down through the excluder . The queen and drones will remain on top. Move the excluder enough so she can walk down into the brood box below.
Here is a good tool to have: I recommend getting a few of them.
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I have some time and about to go out any way, I’ll see if the bee supply has them.
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Dawn when you say clean up the flow frames how do you do that and how do you remove the cocoons?
There are at least 2 options.
The best would be to completely dismantle the frames by undoing the tension wires, wash the frames in hot water and a little dish soap, rinse and then rebuild.
The easiest would be to open and close the cells a few times with the Flow key to try to loosen the cocoons, then rinse with a spray of hot tap water. You may need to fish out some of the cocoons with tweezers or very fine pliers.
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It’s discussed a bit in this thread as well :