Prick the potatoes all over with a fork and bake at 400°F for 45-60 minutes, or until they are fork-tender. Allow them to cool completely, then peel and roughly chop the potato flesh into chunks.
Cook the bacon in a large Dutch oven or heavy-bottomed pot over medium heat until crisp, about 8-10 minutes. Transfer the bacon to a paper towel-lined plate to drain, then crumble it. Pour off all but 2 tablespoons of the bacon grease from the pot.
Melt the butter in the same pot with the reserved bacon grease over medium heat. Whisk in the flour and cook for 1 minute until the mixture is smooth and golden to create a roux.
Slowly pour in the milk and chicken broth while whisking constantly to prevent lumps. Bring the mixture to a gentle simmer and cook for 5-7 minutes, stirring frequently, until it has thickened enough to coat the back of a spoon.
Reduce the heat to low and stir in the chopped baked potatoes, black pepper, and salt. Use a potato masher to break down the potatoes to your desired consistency, leaving some chunks for texture.
Stir in the sour cream and 1 1/2 cups of the shredded cheddar cheese until the cheese is fully melted and the soup is smooth and creamy.
Ladle the soup into bowls and garnish with the remaining 1/2 cup of cheddar cheese, the crumbled bacon, and the fresh chives. Serve immediately.
