So, I have a particularly ornery hive From a captured swarm that I have not yet been able to re-queen. Just to share, I was able to easily do a nighttime harvest of the flow hive without any problems. I think it was better for me and for the bees — well, I know it was better for me. The bees seemed cool with it too.
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Nice idea! I can’t do that because we have so many possums and raccoons that would interfere… 
Are you going to take the Flow super off when the harvest is done? If you don’t, you are risking propolis gumming it up for next season. 
I only emptied 2 frames. Can I keep it on through the San Diego area “winter”? Most of the other frames are only partially filled and there is a lot of unsealed nectar.
I don’t, but you can do what you think is best. 
Most of the traditional beekeepers in San Diego that I have spoken with take all of their supers and queen excluders off between July and September. They leave them off until about February to March, depending on hive stores.
I get propolis even in San Diego “winters” - the bees just seem to go nuts with it, like Halloween candy. 
Don’t want it in my Flow frames, it is really hard to remove. 
You can drain the Flow frames off the hive if it is unsealed, and then feed it back to the bees over the winter. Draining off the hive reduces the risk of leakage. Freeze or refrigerate it though - it may not be ripe, and you don’t want it to ferment.
When my glasses were a bit dirty & I was out of focus, I read this topic to be “nightmare flow hive honey harvest”. I’m glad it was night time & not a nightmare.