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I still can't fathom why this would be going so wrong,, I'll have to test it out here some more, but if my first guess of user error is completely wrong, then...
Removing the book from Calibre then unplugging the Kobo does not clear out the remnants in the database, re-loading the book with the default settings re-uses the original database entry. The Kobo device plugin should have a check option in the "Collections, covers, UPloads" tab to *not* treat replacements as a new book,, you can try unchecking that to see if the bahviour persists.
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