I’m in a sub-tropical climate in Queensland, Australia so I might be of some help to explain what you have happening.
It is simple really and happens regardless of the climate. Honey is moved about in a hive so that there is a constant supply of honey close to the brood area. Honey is also used to insulate the brood and so the outer frame in a brood box is actually honey stores.
Adding a second brood box as changed the lay out of the frames and so the bees have moved honey down from the Flow Frames to be stored in the brood box. That is very normal behavior. In late Spring I have brood out to the inside of the outer frame but the outside of the last frame is always honey.
I hope that explains it clear enough for you.
Now that you have added a second brood box the Flow Super has been moved to the bottom of the list for storing honey in the bees thinking, it is too far away for storing honey to feed the brood when you have introduced a closer location - the second brood box.
Considering your climate, and each to manage their hives as they prefer, but I wonder why you have gone for a double brood box, which is normal in a cold climate, and didn’t decide on making splits to increase the number of hives you have. Food for thought.
Cheers and welcome to the forum Morgan.