Pierce potatoes with a fork; bake at 400° for 1 hour or until tender. Cool. Peel potatoes; coarsely mash.
Lightly spoon flour into dry measuring cups; level with a knife. Place flour in a large Dutch oven; gradually add milk, stirring with a whisk until blended. Cook over medium heat until thick and bubbly (about 8 minutes). Add mashed potatoes, 3/4 cup cheese, salt, and 1/2 teaspoon pepper, stirring until cheese melts. Remove from heat.
Stir in sour cream and 1/2 cup onions. Cook over low heat 10 minutes or until thoroughly heated (do not boil). Ladle 1 1/2 cups soup into each of 8 bowls. Sprinkle each serving with 1 1/2 teaspoons cheese, 1 1/2 teaspoons onions, and about 1 tablespoon bacon. Garnish with cracked pepper, if desired.