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What is not in doubt is that these 'last 3 books' have been transferred from calibre to Kobo as kepubs, not standard epubs. As for why ...
Maybe your calibre library contains both a kepub and an epub for these books and your calibre driver (KoboTouch or KoboTouchExtended) 'File Formats' tab is configured to send kepub with a higher priority than send epub.
Or, maybe you're using the KoboTouchExtended calibre driver and you've configured the Extended tab (by checking the 'Enable Extended Kobo Features' box) to format-shift epub to kepub during the calibre send-to-device process.
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