I moved my library around a few times as I was experimenting with Calibre and suffered the same problem.
Using Windows Explorer I moved all my ebooks to another folder leaving the original folder in place with only the metadata.db alone in it. If any remnants of books are still in the library remove them. Now ADD all the books back into the library and Calibre will recopy the books back to the correct folder and add them back into the library.
Unfortunately if you have multiple formats or separate cover images they will have to be added back manually by editing each books metadata.
Worked for me!
Last edited by Rootman; 10-31-2009 at 11:20 AM.
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