I told you how in the reply above

Shorter version:
install menuhax (so it works) -> boot to
emuNAND -> change theme with the menu provided by nintendo -> reboot console
if menuhax doesnt work again, your NANDs are linked.
If menuhax still works, they're unlinked.
And as far as I know it's safe to unlink them, but I'm not so sure, I'm gonna search for some info about it. ( I think it will format the SDcard )
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EDIT: actually, wait. This doens't use TinyFormat..

Sorry for being a bit confused, I didn't use menuhax and unlinking / linking for quite some time..
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https://github.com/javimadgit/TinyFormat/releases
This is TinyFormat, as far as I know, you just have to get into the homebrew menu from sysNAND (which menuhax would do by default) and then run it. It formats your sysNAND and unlinks the NANDs. The SDcard should be left untouched by it.
I just wanna say I'm not entirely sure about this all, so its better if you look a bit more though the forum about TinyFormat and unlinking before doing this. :S
And if you have any other questions, feel free to ask them!