Position a rack in the middle of the oven and preheat the oven to 400 degrees F.
Pierce the potatoes all over with a fork or the tip of a sharp knife. Place the potatoes directly on the center oven rack and bake until the skins are crispy and a knife easily slides into the potatoes, about 40 minutes. Transfer the potatoes to a wire rack until cool enough to handle, about 10 minutes.
While the potatoes are cooking, put the bacon slices on a wire rack on a baking sheet and cook until crispy, 30 to 35 minutes. Let cool on the rack, then chop finely.
Set the oven to broil. Slice each potato in half lengthwise and use a melon baller or small spoon to scoop out the inside flesh, leaving a 1/4-inch rim intact. Set the flesh aside for another use.
Arrange the potato halves skin-side down on a baking sheet. Brush the exposed insides of the potatoes with the melted butter and sprinkle with salt and pepper. Flip the potatoes and brush with the remaining butter, then flip them back over. Fill each potato with some of the Cheddar and a pinch or 2 of the bacon. Cook until the cheese is bubbly and melted, about 2 minutes.
Top each potato with 1/2 teaspoon creme fraiche and a sprinkling of chives. Serve immediately.