I didn't get much flow August and Sept, but now in Oct the asters have finally gotten going a bit. That's where the smell comes from!!
As to your super...you can leave that on if you want, they'll eventually move up and then next spring start out with brood there and move down.
If that hive has enough in the rest of the hive, then yes, you can take it off, freeze it or let them rob it out. If you let them rob it then all the hives in the area will participate in the spoils. I do this, but I usually try to do this by August because the store from top down and I'd rather have the honey in the top of the brood boxes than in the top of the supers....