Jen asks: " If the deep is now empty of any brood, larvae, eggs, should I remove this deep for this year, bringing the two mediums down to the bench top for winter? "
That's an easy question---if it's empty, definitely remove it.
Then she asks: " if there is still a small amount of brood, larvae, eggs in the deep.. should I leave the hive configuration alone for the winter?"
That's a tougher question to answer. Depending on how much brood etc. are in the deep, you might just leave it alone. You face one of the didfficulties of working with mixed sized frames since you can't move the deep frames up. In an extreme situation you MIGHT consider rearranging by moving the medium frames down, replacing the empty deep frames and removing the medium super. But that is really a tough call. Again, depending on how much is in the deep, you might just prefer to leave things as they are.
It's a call you can only make when you've opened the hive and see what you are facing.