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The Mii characters that can be added by going to Manage Mii Characters, Add a Mii, then Via Nintendo Account are Mii characters that were created on the Nintendo Account that is linked with the app.
Therefore, there is a possibility that the Nintendo Account used to create the Mii character may be different than the account that is linked with the app.
Visit the following page to see how you can check the Nintendo Account e-mail address linked with the app.
I want to check the e-mail address registered with my Nintendo Account.