You can’t. Just like with Nintendo Network. There’s only 2 ways to remove a network account from a 3DS
- Delete the account entirely through the console (it’s in one of the settings menus). But this deletes the account itself, not just the link
- Factory reset the console. This doesn’t delete the account, but it does unlink it. At the cost of losing all your local data
Anything else you do to try and remove it, such as through homebrew or GM9, is not supported by us and we likely won’t give support if something goes wrong. That’s a risk you’d have to take yourself