What happens is the first console will get an error "you cannot use this NNID on this system" when you do the transfer it connects to Nintendo's servers and updates their records of which console has the NNID (adds the new and removes the old) and they don't allow two. Make sense?
Not sure if it was you got my question wrong or I didnt get what you said.
More clearly, my question is
3DS A : Backup NAND (both sys and emu)
3DS A <-> 3DS B : system transfer from emuNAND to emuNAND
3DS A : Restore NAND (both sys and emu)
3DS A and 3DS B : Both playing the eshop games purchased from 3DS A? Safe to go online, eshop, match play, etc., together?