calibre should not delete anything. Are the folders still there? Try using Check Library to locate the non-indexed book folders. You can then move them and add them manually.
One possible problem is that calibre will only rebuild one book per id. Was there an error message when you rebuilt the database? If so, the log might prove enlightening.
Last edited by eschwartz; 09-01-2014 at 02:44 PM.
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