The safest way to update emunand is through system settings.
In all cases you should not update in classic mode, only GW/MT mode.
Do not update by entering eshop and using the prompt that displays when you enter.
Do not update from a rom/game cart.
- Install devmenu/bbm, then use UpdateCDN to get the .cia updates.. (This requires owning a GW or a MT-card)
Here's How: https://gbatemp.net/posts/5375095
If you have a gateway, you can use the latest system menu safely (9.5.0-23)
BUT, If you have an MT-Card, update to 9.4.0 because the multirom menu breaks after that
- Using a second 3ds and download play to send the update that is on a cartridge (I've only heard of this, I don't know if it works)
If you're using the MT launcher and classic mode as emunand, get PBT cfw and install the browser .cia to your sysnand