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You probably need to look at where you have set up your Calibre library. Are you using a Mac or Windows? If you use Windows go into the file Explorer and see if you have the downloaded books in "My Downloads" and another directory where Calibre stores its library. If there is a separate Calibre directory and duplicate copies of all the books you can delete the ones in My Downloads. If this is too technical do you have someone who could look at this on your computer?
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