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You can't "point" Calibre to a nonexistent file - Calibre doesn't operate with virtual files. What you can do is delete all formats from your library after the files with their metadata have been copied over (right-click on the Remove icon -> Remove all formats from selected books); this leaves only metadata in your library. But that means you'll have no way to open the books from inside Calibre, as the files don't exist in the library.
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