What I have found is that if an ebook does not import after being sent to the Kobo, it will still be there and cause issues with future imports. In past, my procedure when an import fails is to remove any ebooks that I sent that were not imported and then to resend in smaller batches until one batch fails. Take that batch and send them one at a time until one does not import.
Since I started opening every epub with Sigil and running it's error checking (including but not limited to epubcheck) before sending to my Kobo devices, I haven't run into an import issue. Hmmm.... that last sentence is just tempting fate.
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