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The only time I've seen that issue was years back and happened when the Kobo was forcibly disconnected (i.e. it was not safely ejected).
As for uploading a lot of books, my suggestion is that your ebooks need to be checked with epubcheck (you can use epubcheck as a plugin in calibre's ebook editor or the Sigil editor) and correcting any errors. My last pass at transferring a large back of ebooks was 12,000 epubs sent to a Clara HD (it has an 128GB µSD card) and while it took quite a while to transfer and import, the process completed successfully.
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