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Sure, you can delete the originals of the files you've added to calibre. As you've realized, calibre has made a copy in its own library structure. It is good to make a backup though, flashdrive or Dropbox or whatever you like. Also, if you decide you don't want to keep one of the formats of the files within calibre, use the 'Remove all formats except...' command from within the 'Remove books' dropdown menu of calibre, rather than manually deleting anything from the calibre file structure.
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