This would only be Honey from supers. I run double deeps for brood boxes and with our shorter milder winters (as compared to many folks on here) with a good couple of weeks with the feeder on top, they seem to over winter well.
The local State Apiarist was amazed that I got (as a new beek) both of my 1st hives through last winter, when many lost theirs. I attribute it chiefly to one thing: from the 1st frost that got the GR last fall, till the 1st hard freeze I kept adding feed. That is also about when they pretty much stopped taking any. The lift told that they where quite heavy by the time they went into winter cold temps.
Whatever they have in the bottom 2 deeps they keep. My question was more targeted at the frames I know are not fully filled, and what to do with what I pull out of them. I think you still kind of answered it though as if the enzymes are not in the mix, it likely is not going to be honey I want to collect. I will just follow my usual "collect anything that is over 3/4 capped", let the bees clean out the other less capped frames.
BTW, what brand system are you running for the Genius hive stuff?