Hi I put our Flow Hive super on in early August. LOTS of bees constantly on it and in the slots but no building out and no honey. Then the other day I started to see a few of the slots ( the individual comb holes…not sure what you call that) about 1/2 full of honey so I thought they were on their way. Just a few mind you. Then I look a few days later and that honey (if that is what is was) was gone? A few other slots were then about 1/2 filled…then the next day or so also gone? Now no honey at all. What could be going on? It is getting too late in the season so I am going to remove it anyway but I do not understand the behavior here. Any thoughts?
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The bees are probably using it as they go. They store it for their own consumption for when nectar outside is light on, also to carry them through the winter. You may find that the bees are constricting the brood, therefore you’ll see more honey & pollen packed around the brood.
As autumn progresses, bees move honey down in the hive towards the brood nest and the areas that they will cluster during winter. That makes it closer for them to reach in cold weather. This is normal bee behavior in late summer and fall. 
Winter starts in mid-late July. What I mean is at that time we need to think about the bees surviving winter. Mite control, removing any supers and leaving them with 2 or 3 deep brood boxes for themselves and the inevitable summer dearth, and winter food storage.
Some hives really have their act together and are able to make a fall human honey crop: Yours probably weren’t one of those because they weren’t ready for a super until August.
Get the bees through winter and next year you’ll get some honey 
Hi - mine did this also when I first added the flow frames. I’m not sure if perhaps I was a little too keen and added the super too soon? Anyway, they seemed to be working on the frames for ages, and would put nectar into the cells and then move it out again. Not sure if they were eating it or just moving around to help mature it ??? (based on my limited knowledge of bees). Eventually, as an experiment I squashed some excess wax I’d scraped off the top of the brood frames into the middle of one of the flow frames. After this, they seemed to finally get working and onto filling the frames. Perhaps a coincidence? What I know is that eventually they started working the frames and when on a flow they filled them fast as anything the second time round (i.e. after they have been cracked for a harvest).
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Good to know. I ASSUME I put it on too late in the year but the two boxes were so jambed with bees it seemed the appropriate next step. I was not planning on extracting honey this season anyway since it is a new hive as of this past June.
I have read here you can leave the Flow Hive super on through the winter, so I figured Id let them build it out to help get them through the winter.
But that has not happenned and I am reading elsewhere now a standard procedure it to remove supers for the winter and collapse the colony down. Since there is really no honey in the Flow Hive super and we are into September, (I am in Missouri by the way), would that be the recommended thing to do?
I would remove it, because bees love to put propolis on things in the Fall and Winter. Propolis really gums up the frame mechanism, and can make it a real challenge to open the frames for the next harvest.