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It sounds as if you tried to use the saem folder for the new library you were creating as the old one? If you are going to go down the route of creating a new library then you also need to use a new folder to store it in. If you did use the same location then when Calibre was adding the books it may well end up not allocating the same internal id for a given book, and thus the apparent duplication at the folder level of books - only the new ones will be referenced by the Calibre database.
If you use the Check Library option under Library Maintenance (accessed via the Library icon on the toolbar)then you will get a report from Calibre telling you which book files it thinks are present but not referenced in its database.
It was not actually necessary for you to do it the way that you attempted. There is an option under Library Maintenance that tells Calibre to rebuild the metadata.db file from the book fies present in the current library location.
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