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I have not been adding books outside of Calibre. The reason for the extra titles is for some reason my metadata.db got corrupted. Calibre would start up and display the books fine but whenever I tried to add a book it, Calibre would freeze. Fortunately my Calibre startup script makes a backup copy of metadata.db so I was able to roll back to a version from a few hours earlier that works fine. But obviously it does not contain any changes made to the library since then.
It would be helpful if Calibre's Check Library offered to move the extra folders out of the library and into a temporary folder so I can then easily add them back. Expecting me to manually find the book folders in the library and move them out myself is unhelpful. Unfortunately due to the library design of a flat one directory per book structure, trying to pick folders out of a 100,000 book library with a file manager is a frustrating experience.
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