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Rename the directory for the old database. That way Calibre won't be able to try to open it. Also create an empty directory for a new database.
If the new database is working with no books, close Calibre and copy all of the directories from the old library to the new library. Then click the icon (in the toolbar) for your new library and select Library maintenance. The select Restore database. This will go through each directory and read the book details from the OPF file and load the database. If that works, you should be good to go.
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