Np
Be methodical - there's a very easy test you can do. Launch gateway and make a change to the menu - create a folder or something. If that folder appears when you boot the 3DS again, then you know that you're in the same nand (i.e. changes after launching gateway affect things before it was launched). In this case, updating would also affect it.
If however the folder does not appear when you boot your 3DS again, it means that change was made on a different menu - a different NAND. In this case you know that changes made after launching gateway, won't affect the system. (so even if you update here, it won't affect the system pre-gateway launch).
Suffice to say, if you don't format EmuNand, then you have one single nand. your regular menu and gateway are all launched on this. Once you format EmuNand, gateway creates a fake nand on the SD card, and launches from that. When you launch gateway, the system nand is hidden, and you run a fake, emulated nand (hence EmuNand for short).
This is why guides are very clear about being absolutely certain you are in EmuNand before updating. If for some reason gateway launched from systemnand and you updated...you'd permanently update your system and lose gateway.