there have been reports of failed updates and partial sysNAND updates, because the update download failed, but still was partially installed and then messed things up... so if you get an unstable internet connection, you might consider letting it download the update in sleep mode on your emuNAND and then, when the message to update pops up in your emuNAND, you ofc decline, go to settings and then install from settings
also, having a 4.x NAND backup should be mandatory for everyone considering to update or change anything on his gateway 3DS, so make sure, you got one
edit:
well there have been a few people, who had a working emuNAND set up and still had this trouble, so better be safe than sorry... I'd still suggest, he lets the 3DS download the full update first instead of finding out later, that his connection is bad