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There is a Tweak that stops files being treated as duplicates, but I personally do not use it as i do not find the duplicate checking reliable enough to want it to happen automatically and possibly overwrite the wrong book.
If you know it is a duplicate then you can highlight the existing record and drag-and-drop the file to the Book Details area. Alternatively you can go into the Edit Metadata dialog and drag the new copy to the Formats area. In both cases it will replace the existing one.
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