["Only problems I have experienced is books with some kind of bad formatting that Kobo couldn't handle and unplugging Kobo from computer before it was safe. I have loaded from one to hundreds books at once. When a bad book keeps kobo from working you will wish fewer books were just loaded."]
I have found that if you load 100 books with Calibre, load them in Author Alpha sort. If a bad book locks up the Kobo it is easy to find the bad book. Just go to the Kobo images folder which is now in author/book sort and find the last book loaded that has the full set of images. The next book is the bad one which can then be identified in Calibre and removed or fixed.
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