Yeah there's a way to remove the nnid from the nand, i have it here somewhere in my notepad. Will have a look for it.
That nnid will be rendered useless though (not really a problem going by your post there) because they're not only linked on the console but also server side.
I've done it before on emunand and it was basically like it never existed.
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Found it!

Old notes i found on here a fair while ago in some thread...
Code:
My 9.4.0 emuNAND already has NNID and you need internet/actual
fw to remove it, so i thought about a way to remove it without internet.
NNID is listed in: \data\<your unique id>\sysdata\00010038 > 00000000
It was pretty simple to do it and here it is how i did it:
1. I extracted my fat16 xorpad using launcher.dat from 3DS_Multi_Decryptor
2. Dumped emuNAND.bin using emuNANDTool
3. Extracted emunand.fat16.bin
4. xor'ed emunand.fat16.bin
5. Mounted emunand.fat16.bin.out with WinImage
6. Browsed to \data\<your unique id>\sysdata\00010038
7. Replaced 00000000 with another one i've extracted the same way that never had nnid
8. Renamed emunand.fat16.bin.out to test.bin
9. xor'ed test.bin
10. Injected test.bin.out into emunand.fat16.bin with HxD
11. Injected emunand.fat16.bin @ offset B930000 with HxD
12. Injected my new emunand.fat16.bin into my SD Card using emuNANDTool
Eh, voila, after booting into emuNAND NNID was gone :)
I could have switched out or deleted any other files i wanted,
maybe this will help your research
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Don't remember if i did it on n3ds or not, pretty sure i did it on o3ds but it may still be helpful.