I don't think calibre deleted any books. I suspect that they were deleted as the library was copied/moved between different filesystems, and that calibre was used to copy the library at one step. And some books then were left behind and later deleted.
Keep the library on a local filesystem and don't switch between Linux and Windows. Then you should have no problems. If you update the library in Linux then Windows has no problem using a copy of that library, but if you update the library in Windows, then Linux may not be able to access some books.
Last edited by Adoby; 03-26-2014 at 10:22 PM.
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