The issue, if I recall the details correctly, is that the Kobo stores details of its library in a SQLite database, and it certainly used to be the case that if you did things even slightly wrongly with Calibre, the database would be corrupted, and all your books would thereby disappear. It may well be that this issue has been sorted out now - the OP can probably get more details in the Calibre forum.
Last edited by HarryT; 07-07-2013 at 03:13 PM.
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