Whenever I am considering harvesting them. That is usually when the end window shows a lot of full cells, or our Arnia hive scale shows a 15 to 18kg gain in weight (the Flow super can hold up to 18kg of honey). The side window is the last to be capped, and I am willing to extract one frame at a time, so I don’t wait for that one. 
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If I was the OP- I wouldn’t attempt to reset the frames at this stage. The reason being if you did that you would break a lot of the wax and with the unripe honey- I think you’d end up with quite a bit seeping into the extraction channel.
Our first year we had some rows like that- and the bees work around them OK- and even finally fill them to a degree- making lopsided cells where they can. There is a chance that those cells which never get capped will cause soem leakage when the frames are harvested but not too much. Best to wait until after the next harvest before attempting to re-set them I would say…
I agree it is a possible risk, but it didn’t happen with mine. The wonky channels reset and the others stayed intact. I was very careful though, and used 2 keys at once to avoid any torque putting a shear force on the frame.
So now you’re an engineer also?
The thing to try would be for someone to try the key in the top slot when harvesting and see if any honey leaks into the channel before commencing harvesting.
However it seems there’s more to it.
@cyberph are these founding frames?
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No, I am just innately annoying. 
I have a few weird characteristics. You have probably heard of musicians who have “perfect pitch”. I don’t. But I have this odd thing of “near perfect timing”. So, I can wake myself within 10 minutes, without an alarm (no I don’t trust it). I can set a mental timer for cooking and it goes off within 30 seconds of an electronic timer (no I don’t trust it, wine and conversation warp it!).
Equally I have a 3-D spacial perception ability which is pretty accurate at working out whether something will fit into a limited space, and whether doing something (like twisting a key on one side) will twist the whole structure as it accommodates to the space the key is demanding. I am not saying it is accurate. It is just an intuition. In real life, it works far more often than not, but that is not 100%. On the other hand, neither is engineering 100% accurate, that is why they all have OCD… 
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I have done that. By accident. I forgot which channel the key went into. It was a long time since reading the instructions, OK? However, I was using 2 Flow keys. So the twisting on the frame should be minimal.
None leaked. At all. I waited for 20 minutes for the flow to start… 
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yes they are from 2015 founding offer
Hi cyberph,
So nice to see that nectar is being stored. Im sorry to see that 2 inner segments are misaligned. As you have mentioned that the cells didnt reset when putting the Flow key into the upper slot, I would advise getting in touch with the Flow Team via email info@honeyflow.com. When it comes to harvest time, you may find the bees wax these cells up regardless, or even try to store honey in them. To best avoid honey leaking, I would insert the Flow Key in part way and harvest the honey in front of the misaligned cells. Then once the flow lessens harvest the remainder.
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