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.
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.
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.
