Another book went missing so I figured it must be a corrupt database. I factory reset the Nook, and then I was able to add the same books that wouldn't show previously.
I went to recreate my shelves and discovered the previously used shelf names are now "burned". They don't show on the reset nook because they only contained sideloaded books. But when I try to reuse an old shelf name when creating a new one, I'm told there is already a shelf with that name. Same goes for trying to rename a shelf once created. Grrr! So I guess the lesson is to delete any shelves that only have sideloaded books and sync before factory resetting the Nook. Otherwise, you'll forever have these burned phantom shelves associated with your account. Luckily I only had 3, and I was able to slightly alter the name to recreate the two I still want.
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