I'm not sure what you actually want to do, since Calibre has no facilities for any syncing of books. The only thing automatically sent are downloaded news, and those are sent to the first device connected.
That said, why not just add tags to the books according to what device you want to send them to and use your idea with saved searches? If you tagged the books you want on the Nook with, say, "Nook", you could have a search
Code:
tags:"Nook" and ondevice:false
that would display the books you want to transfer to the Nook if that device is connected- I don't see where you'd have to change the search, just create one for each device.
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this plugin, although, from what I understand, it sends to the next connected device, as well, in the same manner the news do.