Cook bacon in Dutch oven over medium heat until crisp, about 8 minutes. While bacon is cooking, use vegetable peeler to remove wide strips of potato peel; reserve peels. Cut peeled potatoes into 3/4-inch pieces. Using slotted spoon, transfer bacon to plate lined with paper towels. Add reserved potato skins to bacon fat in pot and cook until crisp, about 8 minutes. Using slotted spoon, transfer potato skins to plate with bacon.
Add onion to fat remaining in pot and cook over medium heat until golden, about 6 minutes. Stir in garlic and flour and cook until fragrant, about 1 minute. Gradually whisk in broth and cream, stir in thyme and potatoes, and bring to boil over high heat. Reduce heat to medium-low, cover pot, and cook until potatoes are tender, about 7 minutes.
Discard thyme and transfer 2 cups cooked potatoes to bowl. Puree remaining soup in batches in blender until smooth. Return to pot and warm over medium-high heat. Off heat, stir in cheese until melted, then whisk in sour cream. Return reserved potatoes to pot and season soup with pepper. Ladle soup into bowls, garnishing with bacon, fried potato skins, scallions, cheese, and sour cream.
To reheat leftover portions, gently warm the soup in a saucepan over medium heat until steaming. Do not let the soup boil, which will cause the sour cream to separate.