Nintendo is known for rather draconian copyright tactics even if they don't have the proper ownership of a derivative work. Though the notice was on the game as a whole, which could be a more infringing case even if a it's fan-made game. I would take the chance on just the music if you and the owner think it's different enough from any official version.
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"All I want is a pretty girl, a decent meal, and the right to shoot lightning at fools."
-Anders (Dragon Age: Origins - Awakening)
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