I am going to answer my own question, at least partially.
About nine months ago, way before the sequence I described in the OP, I took a backup of my MO Folder. It stayed in place on my hard drive. At some later point, but before the OP events, for some reason MO's profiles folder setting was set to this backup. I have no recollection of doing this, I can only assume MO has a way of searching for a folder and if it finds one that matches various criteria, it chooses it. The fact that this setting was in place for some time is revealed by the fact that most of my Mod settings made in the intervening period were made in the backup folder, not in my c:\Games\ModOrganizer folder. I failed to notice this.
So recently when I thought I was cleaning the slate by moving the NO folders to an offline drive, I was actually doing nothing of the kind. That information survived in the backup folder, and all my problems ensued.
