I need to know this to, when I move from emuNAND from a 3DS to a N3DS.
I'm guessing you can't back-up and inject the emuNAND to a diffrent 3DS due to encryption, so a system transfer might be the only way. I did a transfer resently from 3DS to N3DS in sysNAND and the only requirement is that it must be at the latest firmware, and it didn't reboot during the process untill completed.
Edit: System Transfer might not work due to NNID. Can the 3DS work with a sysNAND and emuNAND on the SAME HARDWARE being diffrent? Not sure how the eStore/WiiVerse does it's checking (like does it have a serial number burnt into the board/MAC address etc)