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I'm just in the process of setting up a Kindle bought as a gift for my Father-in-law. My copy of Calibre has a library set up for my own Kindle.
All I did for the new one was create a new, empty library and filled it with the books I intend to populate his Kindle with, which included sending copies from my library to the new one. It seems to work at treat, so I doubt you'll have problems with a Kindle and a Nook if you want to use separate libraries with separate readers.
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