I have also experienced this when I try to import more than ~250 books in one batch. In my case, it wasn't because a book contained errors, because when I limited the import to 100 books at a time, everything worked flawlessly. I suspected the Kobo was timing out or going to sleep before it finished importing, so I tried setting the reader to "Never sleep" but that didn't help. Now I limit the number of books I transfer to ~200 at a time. That seems to work.
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