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Maybe I'm barking up the wrong tree, but I assume you've deleted the books from the Kobo between attempts with Calibre? At one point it seems like you were saying you'd gotten the files transferred as SERIES - INDEX - Title in the Title field, but the Kobo still wouldn't sort them that way? That would seem to be a Kobo problem? Have you tried power cycling the Kobo after the transfers or setting the Shelf to display by Author or Title?
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