So far, that didn't happen to me. But I haven't put that many books in the first place, since I'm still trying to figure a couple of things out.
I'd say that I may have added 15 documents (proper ebooks, text documents converted in .epub, a couple of PDF) and removed half of them. Not once a document disappeared after the transfer.
How do you load them? Via Calibre? Or do you drag-and-drop them?
Best of luck in figuring out what's happening fast
