1. Prick potatoes all over with a fork; microwave on high until cooked through, turning once, 12 to 15 minutes total. Let cool slightly and scoop out flesh, discarding skins. Mash with a fork. In a large skillet, cook bacon until crisp, turning once, about 10 minutes total. Let cool, then crumble.
2. Melt butter in a large saucepan over medium heat. Add flour and whisk until smooth and light golden, about 2 minutes. Slowly whisk in milk and cook, whisking, until thickened, 5 to 6 minutes.
3. Stir in cheese, potatoes and 1/2 tsp. each salt and pepper. Cook, stirring, until cheese melts and soup is heated through. Whisk in sour cream. Check seasoning and add additional salt and pepper if desired. Divide among 6 soup bowls and sprinkle each with bacon and chives.