Pierce potatoes with fork; place on microwave-safe paper towel or roasting rack in microwave. Microwave on HIGH for 15 to 20 minutes or until tender, turning once halfway through cooking. Cool slightly.
Meanwhile, cook bacon in Dutch oven over medium heat until crisp. Remove from Dutch oven; drain on paper towels. Crumble; set aside.
In same Dutch oven, combine milk and flour; blend well. Cook over medium heat about 15 minutes or until bubbly and thickened, stirring frequently. Remove from heat.
Cut cooked potatoes in half. Scoop out cooked potato from skins; place in medium bowl. Discard skins. Mash potatoes well.
Add potatoes, bacon, 2 tablespoons of the onions, 1 cup of the cheese, salt and pepper to milk mixture. Cook and stir until cheese is melted. Add sour cream; cook and stir until soup is thoroughly heated.
To serve, spoon soup into individual bowls. Sprinkle each with remaining onions and cheese.