Preheat oven to 350 degrees.
Cook the bacon in a large skillet over medium heat until crisp, then remove and crumble once cool enough to handle.
Leave ¼ cup of bacon grease in the skillet and set the heat to low. Sprinkle in the flour and whisk for two minutes. Slowly add splashes of milk, while still whisking, until all milk has been added.
Place sour cream in a medium sized bowl and then temper it with the warmed sauce by stirring in a few splashes of sauce at a time until the cream has transformed into a warm liquid, then combine entirely with the sauce.
Add cheese, bacon pieces, chives, salt, and black pepper to the cream sauce, then pour over the potatoes in a large dish. Toss gently to ensure the potatoes are fully coated, then pour everything into a 9x13 baking dish and spread into an even layer.
Cover the baking dish with foil and bake for 30 minutes. Remove the foil and bake for an additional 45 minutes, until the potatoes are tender and the cheese is golden brown.
Remove from oven, let cool slightly, and serve.