What do you do with a brood nest that is packed with capped honey before the fall flow?Much of that decision is where you are located, what flows you have, etc.
In my part of NY the first pull is over and the fall flow has begun. I would be careful of leaving them un-supered if a flow is going on. They will harvest nectar and plug up the brood nest. I never want to see my supers 100% capped. It means they have run out of room and they need the extra space to dry out nectar.
In any event I would extract and put them back on, at the very least for them to clean them up. supers off a colony this time year are a moth magnet so at least the ladies can defend and clean them. I pull summer honey before goldenrod and bamboo start blooming. Fall honey here crystalizes in a heartbeat.