Nope, the Kobo Desktop sync didn't help, but I did get it solved by renaming the Shelf in Calibre and then letting Calibre sync the metadata again.
When I originally tagged the books in the Fiction category, I selected a batch at a time, and at least sometimes I retyped "Fiction" rather than picking the existing value from the dropdown. Is it possible that in doing so I created several different shelf tags, all with the same text value? And then Calibre grouped them correctly by text value, but the Touch treated them as separate shelves (but obviously got confused and included all the books on every shelf)?
That would explain why renaming the shelf fixed it - it regrouped all the books under a single tag.
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