Bake potatoes as desired. Allow them to cook, then peel and coarsely mash them. Set aside.
Place flour in a large Dutch oven. Gradually add milk, whisking until the flour is blended. Heat the milk mixture over medium heat until it is thick and bubbly, stirring occasionally, about 10 minutes.
Add the mashed potatoes, most of the cheese, salt and pepper. Heat, stirring constantly, until the cheese melts. Remove from heat. Stir in sour cream and cook over low heat for 10 minutes or until heated through; do not boil.
To serve, ladle soup into bowls and garnish as desired with cheese, green onions or chives and bacon.