Cluster is in the top deep and the bottom deep is nearly empty — swap the boxes, remove one, or leave it for winter?

Vermont, second year, two hives on double deeps. Went through hive one on Sunday: all the bees, the brood and most of the honey are in the top deep. The bottom deep has drawn comb, some old pollen, a little honey in two corners, and hardly any bees. It's basically empty. I've read three different answers. One: swap the boxes so the cluster is on the bottom and can move up into stores. Two: pull the empty box and overwinter in a single deep. Three: leave it, they'll sort it out. My club mentor says "heft it" but I want to understand the logic, not just the answer. Does an empty deep under the cluster hurt anything? And if I swap now, do they actually fill the empty top box with syrup at this point in the season? Daytime highs are still mid-60s°F this week, nights in the 40s.