Bake the potatoes at 375 degrees for one hour. Let sit until cool enough to handle. You can bake the potatoes a few hours or even a few days in advance.
Melt the butter in a large saucepan over medium-high heat until it begins to brown. Stir in the flour thoroughly. Cook for 2-3 minutes until the mixture is smooth and starting to brown. Stir in the milk, one cup at a time, until blended thoroughly.
Stir in the chopped baked potatoes and onion. Bring the mixture to a simmer, stirring occasionally. Simmer for 5 minutes.
Reduce the heat to low. Add the cheese and sour cream. Crumble in the bacon in small pieces. Mix thoroughly. Simmer for 1-2 minutes until the cheese and sour cream have melted.
Season to taste with salt and pepper. Serve immediately.