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Books you buy from B&N and download through the device are stored on a hidden partition that isn't accessible to Calibre. It is unfortunate, and there's no way to change it (though you can "root" the device and run a standard version of Android, and have complete control, but I don't think that will let you buy from B&N the same way as the stock device). You could turn off the WiFi on the nook, and treat it just like your Sony, which is to say, buy through B&N's web site, download it, import it to Calibre, and transfer it to the nook, but again, that loses the convenience of shopping directly from the device.
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