First time Beek.
I am also having issues with my bees not storing honey in the Flow frames.
I received the Flow in late March and installed my package in late April.
They flourished and filled the 8 frames inside the Deep hive box in about 6 weeks.
So I purchased another Deep Mid-June to put between the first one and the Flow.
During this period there began interest in the Flow frames, but the bees were mostly filling up the second Deep.
As of last week all 8 frames on the second Deep were full…and mostly capped honey. Each frame weighed about 17lbs.
They are definitely interested in the Flow frames, actively sealing the gaps and propolising, but not yet drawing out the cells. At any given time there are 200-300 bees on each Flow. I did coat them with melted burrcomb (discarded).
Perhaps they filled up the second Deep with enough honey they do not require the Flow yet?
Also, at what point to I remove the Flow frames for winter (Ohio)?
If the Flow gets pulled for winter then why bother keeping it on the Hive past Sept?
Should I just pull it now and put a medium or two on for winter?
Concerned,
-Armothe
Given a choice between wax and plastic, bees will almost always go for wax first. You did the right thing to put a second deep on there. In Ohio, your bees will need those stores for overwintering successfully. They will probably not use the Flow frames until they are overflowing and really cramped for space. That is totally normal in the first season. Once the frames have been used, they will refill them much more quickly next time.
When your nectar flow is over for the year. Your local beekeepers would be the best to tell you this, but I would say late August is a good bet.
You shouldn’t. Especially as it creates more overhead dead space for the bees to keep warm. Take it off and store it somewhere out of direct sunlight.
I always put boxes on one at a time. Too much space means that the bees have to defend more space with insufficient workers. I wait until each box is at least 80% full before adding another box. That way, they have more bees to fight off Small Hive Beetles (in the middle of your second photo), wax moths and other pests.
You could put a medium on, but I would be tempted to leave them with the Flow frames, so that they continue to get coated with bee pheromones. If they actually store any honey in there, you can harvest it, even if it is unripe. You could then freeze it (preventing fermentation) and feed it back to the bees as needed over winter.
Hope that helps. Please let us know what you decide to do! 
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Thank you for the advice!
The second deep is chock full of honey and a medium super was added with only 4 frames (two on either side) leaving the middle area for some sugar bricks. Depending on if they fill the 4 frames quickly I may add another two frames. I removed the queen excluder since she already has a sturdy horizon over her and left the Flow frames on (at least for a bit). When adding the medium the bees were very defensive of the Flow frames, even though they did not have any honey in them.
