I'd recommend making an emuNAND backup with
EmuNAND Tool before updating your emuNAND, just in case anything goes wrong.
Don't update from the pop-up, always update from system settings.
Enter system settings and make sure you are in emuNAND. Don't leave the system settings or you will be booted back into sysNAND. From system settings go to other settings and press the arrow on the right a few times until you see system update. Select it and it will update your emuNAND to the latest version. Be sure you're using the latest Gateway launcher!