I've had my books disappear from the Kobo after uploading a new book to it even after ejecting it properly. It was strange; I added a book, ejected the Kobo and then when I turned it on their were no books in the library, nothing. They came back after I powered it down and back on though.
I did have to do a factory reset though to solve another issue (book in my library that I couldn't open or delete). Not a great start.
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