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Somehow, I had one version of my Mii on my Wii, and one version on my 3DS. When configuring my Wii U, I used the 3DS version, since that was the only one I could import on initial setup. After importing Miis and save data from my Wii, I then deleted the duplicate version of my Mii that had been copied from the Wii out of the Wii U's Mii storage.

However, I noticed now that when I boot up Super Mario Galaxy 2 on my Wii U, my save file just shows Mario, not my Mii. Did I accidentally delete my Mii (and thus any Wii Sports save data and any other Wii save data that requires a Mii) from my Wii U's Wii menu as well as from the Wii U's own Mii storage?

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Even though they are "duplicate" Miis as far as you are concerned, they are 2 separate Miis as far as the system is concerned.

If you deleted the Mii that was imported from the 3DS, then any content tied to that Mii would be gone. Consequently if you deleted the Mii that was imported from the Wii, then any content tied to that Mii would be gone. Ergo, if you deleted the Mii that was imported from the Wii, then that would cause your Super Mario Galaxy 2 to revert as well as any Wii-specific data.

I tried this by "duplicating" a Mii using my 3DS, original Wii, and Wii U.

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When I transferred my own data from the Wii to the Wii U it seemed that, although all Miis and save files were transferred, some save files after the transfer were not associated with their Miis on the Wii U.

In the Wii Menu of your Wii U, open the Mii channel and see if the Mii is still there -if I'm right, it should be. Reassigning it to the save file may be do-able depending on the game. IIRC Mario Galaxy 2 allows you to change the assigned Mii.

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I believe it would only delete the Mii from Wii mode, NOT the Wii U's Mii storage.

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    Of course, Super Mario Galaxy 2 is a Wii game... – Powerlord Jan 16 '15 at 1:02

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