Hi Faroe,
I didn’t have to do anything to remove the brood from the flowframes.
I simply allowed the brood to hatch and the queen migrated back down to the lower boxes on her own and the upper flow-frames were taken over once again with honey stores and it did function a little stiff on the first honey cycle, but has been fine since.
I had left flowsupers on three colonies and none of them had queen excluders in place. Only one of the three ended up with brood in the frames, the other two were used by the bees, exclusively for honey stores.
This winter, after the autumn flowframe harvest, I removed all flow-supers from every hive and staged them nearby for honey bee cleanup prior to putting them in storage. All is going well and we will just restore the flow-supers when the spring nectar flow is in full swing and the lower boxes are filling with the queens laying where they are expected to.
Sorry I have been absent from the forum for quite a while. I wish you all the best! Fred