In layman terms, when you unplugged and "changed some stuff around" Windows reinstalled your USB devices to new paths so they weren't where AH thought they were. Think about getting all of your mail into a new address after you've moved, same thing.
Renaming the "settings" folder forced AH to build a new one from scratch, searching the devices in their new locations etc. Entirely deleting the "settings" folder would have given the same result, however renaming saves the old settings for potential further investigation.