Place the potatoes on a roasting tray and bake for 45 minutes. When done, the tip of a paring knife should go through the potatoes easily.
Slice the bacon into lardons (thin strips) and cook in a large, heavy-bottomed pot over medium heat until crisp. Remove the bacon from the pot with a slotted spoon and set aside, leaving the drippings in the pot.
Add the flour to the drippings in the pot and stir to combine. Cook, without adding color, until the flour and fat has combined, about 1 minute. Pour in the milk while you whisk to incorporate. Cook over medium heat until bubbly and thickened, stirring frequently, about 15 minutes.
Scoop out the potato pulp from the skins and add to the milk mixture. Mash with the back of a wooden spoon leaving it a little bit chunky.
Add the cooked bacon (leaving a little out for garnishing the soup), 1 cup of the cheese, and season well with salt and pepper. Stir until the cheese has melted. Remove from the heat.
Ladle the soup into bowls, drizzle with sour cream, sprinkle with remaining bacon bits, grated cheese and chives.