Explain my old 3DS XL situation then please. Because I had bought the Gateway for that system, had no clue what unlinking was, went in, updated the EmuNand, and restarted the system. Only to relize I couldn't go back into Gateway. At this time, 9.9 was the highest update.
You can update even with linked NANDS. No idea what happened to you, but just did it a few moments ago for someone's 2DS. Formatted emunand for them, booted emunand, then updated to 10.3.
In my Old3DS, I already did a lot of system updates after just make a clean emunand (using gateway menu). All was fine.
I don't know for you though, but keep in mind that every times you exit the system settings in emunand, you're kicked to sysnand.
Did you do this:
1. Boot to emuNAND
2. Go to system settings
3. At no time leave the system settings
4. Check it says something other than "Ver." Before the firmware
5. Go to other settings, system update. Leave it alone until updated
Did you do this:
1. Boot to emuNAND
2. Go to system settings
3. At no time leave the system settings
4. Check it says something other than "Ver." Before the firmware
5. Go to other settings, system update. Leave it alone until updated