Toss the Gruyere and Emmental with the flour in a medium bowl.
Combine the wine and garlic in a fondue pot or medium saucepan and bring to a simmer. Gradually add the cheese mixture while stirring constantly, simmering until the cheese is incorporated and thoroughly melted. Stir in the mustard, nutmeg and cherry brandy if using.
If you are using a fondue pot, set it over its burner. Otherwise, pour the mixture into a slow cooker and set it to "warm." Serve with an assortment of dippers such as baguette cubes, sliced vegetables and sliced fruit.