I've never seen this posted before, so I thought I would make a thread about it.
If you have blank internet settings in sysNand, and then configure the internet in emuNand, the settings will carry over. I noticed this while setting up a N3DS, but it also applies on the O3DS. This is true even if nands are unlinked. Before setting up internet on emuNand, make sure you have fake Wi-Fi connections on sysNand so it can't overwrite.
If you have blank internet settings in sysNand, and then configure the internet in emuNand, the settings will carry over. I noticed this while setting up a N3DS, but it also applies on the O3DS. This is true even if nands are unlinked. Before setting up internet on emuNand, make sure you have fake Wi-Fi connections on sysNand so it can't overwrite.