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I have no idea why you would have lost those books, but the first thing I would do is run Check Library, including checking if the files match the database.
It's possible the actual ebook files are still there, just missing in the library. If this is the case, they'll show up in the Check Library, and at worst you would have to move them out of the library folder and re-add them to Calibre. You would lose the metadata but at least you would have the books.
One other idea: are you certain you're looking at the right library? I know that sounds like a dumb question, but you'd be surprised how often the solution to computer problems is something obvious like that. (Like having a password fail because you have Caps Lock turned on)
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