I would probably feed them the shallow back over the inner cover, then remove it. Otherwise, the shallow will be the brood nest next spring. While thats not a disaster, it can be a problem if you need to swap around brood frames etc next spring.
Here on the Wasatch, after extracting in late July, I give them back the supers over the inner cover to clean up, and protect for me. The evening temps start dropping in Sept, and they start pulling everything down into the brood nest. (In the 40's the last few mornings) I give them a heft, and try to equalize, determine feeding requirements. In any case, I cut them down to 2 deeps. I pull the cleaned out supers when we get freezing temps, and store them for next year. It has worked well, and they are going gangbusters when the fruit bloom starts. I usually make up some fondant, just in case, but the winters haven't been too bad lately.