I recently wrote about 3 drone cells in my flow. So now that the worker bees of takien care of those 3 cells, I went out this morning to check it. What do I see? I see my Queen is in my flow. Now what I do? I seriously need that metal queen excluder now. I ordered it late last week. Do I pick up the queen with my fingers and place her below?
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Well done to you for finding her! Mystery solved. 
I would remove the queen excluder ASAP. You never know, the queen may move back down of her own accord, relieving you of that responsibility. You can then deal with her if needed, when your new excluder arrives.
You can pick up queens with your fingers, but it takes some skill. If you are going to do it, approach her from behind to scare her as little as possible, and gently grip her by the wings. It is pretty tricky not to damage her, so be careful!
I actually use a one-handed queen catcher from Mann Lake, and I love it.
Other people like these (but don’t buy the crappy plastic version, they break very easily just when you need them):
If you don’t have either of these, and you don’t want to risk picking her up with your fingers (very hard to do with gloves, by the way), then there is another simple option. Take the Flow super off the hive and set it on top of an inner cover next to hive. Find a frame of brood in the boxes under the super. Leave that frame in the brood box, but note where it is. Place the frame with the queen with one corner or edge resting on the brood frame. Gently puff a little smoke above the queen to encourage her to go down into the lower box. She usually will, as queens prefer dark hive areas to those in bright sunlight. They also hate smoke more than most other bees, so you really shouldn’t need much smoke to make it work.
That method works pretty well. You should check the frame visually after you think she went down though. Queens are tricky things, and sometimes they sneakily just run to the other side of the frame you are trying to move them from.
Hope that helps. Another nail in the coffin of Flow’s queen excluder design. We should tell @Freebee2. 
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My queen excluder was delivered right after I posted the above. We placed the new metal excluder. So before we placed it, we found the queen. I actually watched some YouTube videos on how to pick up the queen and I did it. I placed her in the super below. Unfortunately, who knows how long she’s been in there but it was definately long enough to lay all kinds of brood. They were in various stages. I’m upset because there was so much honey capped and now the flow is a hot mess.
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Thank you for this information. I was lucky this one time picking her up but I’ll order the catcher for future instances.
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The honey will stay or be moved by the bees and after time the baby bees will be born and then finally the bees will store honey in it. Its not going to be a mess forever. 
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Thank goodness. I was very worried. I was a little defeated after seeing it yesterday.
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In our case, it’s bees who laugh at our plans…
I read thru some of your other postings about the drone cells a couple days ago, but can’t recall if the possibility that your colony needs to be split was discussed? Just thinking you might want to check the brood box for space issues that could lead to swarm prep and consider splitting, especially now that your harvest plans have been altered a bit 
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The bees were definately laughing at me. The middle box has plenty of room to lay. Next hive visit, we’ll check all. Thank you for the suggestion.
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