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I have had exactly this problem on my Kobo Touch after taking a book off because I have found a cover for it, and then trying to put it back on. I could load the book by going into the calibre library folder in Finder (Mac) which I'm guessing is the same as Windows Explorer referred to above. Then I just pulled across the folder for the book, which contains text, cover and whatever else goes with these (sorry, very non-technical!).
However, I have never had the problem of all books disappearing from the Kobo but calibre marking them as being in the Kobo library. It would just indicate that the book wasn't in the Kobo when I linked them up again.
It sounds as if you need to do a Factory Reset and start again, maybe just loading a few books at a time.
Good luck!
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