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I've imported and converted some pdfs to epub in calibre, with variable results. After the convert the book listing/metadata box on the right shows the various formats I have in the database for that book. If I click on the blue link to the epub format it opens the book with the calibre reader. If I click on the blue link to the pdf format it opens in Acrobat Reader, the program associated with pdfs on my machine. In your case that might be the Nuance program.
So clicking on the link to the specific format rather than just using the "View" option should open the book in the reader associated with that format. It hasn't added any dupes, for me at least.
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