[ficbot]

I think tags would be your friend here. Each book could have more than one tag, but the file would not need to be copied multiple times. This is what my sister does, I think. She imports all the books in Calibre and then tags them both by genre and by person who would read it. So a book may have only her name, only her daughter's name or both. When she wants to load only books for the kid, she just searches for the name and voila, there they all are.

ETA: I read again and see that you are talking about copying files directly. What you want to do is tag the books as I described, do a search for the tag so you are only seeing the books for, say, Child A, and then copy those books to a directory. Highlight your search results, right-click, and you'll see options to save a single format into a single directory. Then you should be able to copy files from that directory into the Nook.