So...
Did a factory reset. Interestingly enough (and this may happen for everybody, I don't know), right after the reset, my shelves area was completely empty (yes, I did a synch). Then, when I went to add a shelf once I started going through my books--bam, my shelves appeared.
Unfortunately, they appeared still with the duplicates. But also something interesting there now, too.
I used the wrench to choose the option to only show books on my ereader. When I went into the offending multiple shelves to delete books and empty them--surprise! The ereader tells me they're already empty.
Also related--if I have shelves that previously contained kepubs, there's something else interesting. If I'm viewing my list of shelves, it will say something like "6 books". But when I actually go into the shelf itself, the number of books in it only lists the ones on my ereader (which makes it the accurate count).
So obviously, whatever books are still "stuck" in the shelves are the ones I've purchased from Kobo, not anything I've sideloaded myself.
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