2 Queens, some more honey and preparations for Autumn

Thank goodness, our new Queen has been accepted by the queenless hive... Not only that but she is laying like a trooper and is wonderfully easy to spot thanks to her bright mark (thank you Donald).

Once the hurdle of requeening was out of the way, we proceeded to take off the supers from the hive (we were reluctant to make too many changes at once). We took 4 supers off but none were completely full and only about half were capped. Still, we managed to extract about 20 pounds of honey which is still in the honey bucket for now. This harvest is much darker than the Spring yield and the consensus seems to be that it has a more complex taste.

We are now at the point where the bees have cleaned out the super frames and we are feeding both hives - one at a time as we only have the one (small!) feeder. We have also put Apilife var on both colonies. I was a bit concerned - apparently the colony may become "slightly agitated" during treatment.... However, so far, we have not noticed any reaction. It also says that they might take down less food - fingers crossed as both colonies definitely need it (neither has ten fully drawn out brood frames - I was hoping that the feeding would make them draw them out).

Question: Some of my super frames still have pollen in - am I ok to leave them wrapped in bin liners over the winter or will the pollen go mouldy? Does it matter?