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Eventually figured it out by, after having loaded both books from Calibre and the Kobo store, deleting the book .sqlite database and so the Kobo rebuilt it with both. The database in now functional and isn't corrupting anymore, and the books are matched and can get updated metadata with KoboUtilities. Of note is that I do still get a errors in Calibre if it is the 2nd (or more) time mounting my Kobo in the same Nickel session (i.e. haven't quit Nickel/shut down between mounts).
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