Hi_ finally after two years I have capped honey in middle three frames of the Flow super. They have not filled all the way to front and back of the frames, nor on outer frames… I have two deeps full below the Flow. I plan to harvest whats in the flow frames before winter prep when I will remove the Flow box. My girls are busy herding SHB in and out of The empty cells at back of box ( I see them through the observation panel ) When I go to harvest thiose frames I am assuming SHB in those frames will end up in my honey? Do I just strain? Will it contaminate my honey? I haven’t ever harvested as I’ve left all for the bees so I am a newbee when it comes to extraction of any kind. Thanks for any advice.
They may do that, yes. Others have seen that. A bit gross, but then honey is never a sterile product. If you see bits that you don’t like, straining should work just fine. I would harvest soon though, the bees will soon be in the mode to pull the honey down into the brood boxes. I did my last harvest in late July. 
Thanks, Dawn. That information helps ! Right now we have a fall flow of goldenrod and jap. knotweed - I live next to a park of 200 acres with forest, meadows and with all kinds of goodies blooming. I’m taking advantage of that with flow frames - but if they need to take it down below I’m happy for them to do that : ) I am new and so far my phIlosophy is for them to always have two boxes for themselves and if extra I will harvest if it seems they have enough. last year that worked well and they got through winter just fine. I haven’t harvested for myself yet and as I work more with the bees I find my attitude has shifted. If I never feel there is enough for me to harvest and they need it all I am fine with that. But I will also be happy to have a little for myself as I spend a Boatload of money buying honey from other local beekeepers! 
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