Heat the oven to 425 degrees F. Put the potatoes on a large baking sheet and toss with the olive oil. Sprinkle with 1 teaspoon of the thyme, 1 teaspoon salt, 1/2 teaspoon pepper, and toss again. Bake the potatoes until they feel perfectly tender when pierced with a skewer, 20 to 25 minutes. Remove from the oven and let rest until cool enough to handle, about 10 minutes. If not working ahead, increase the oven temperature to 450 degrees F.

Carefully hollow out each potato: Begin by slicing off the top; use a small spoon or a melon baller to scoop out most of the flesh inside, transferring it to a large bowl. Discard the tops. Mash the potato flesh with a masher or a fork, then combine it with the bacon, 1/4 cup of the chives, the creme fraiche, the remaining 1 teaspoon thyme, 1/2 teaspoon salt, and 1/4 teaspoon pepper. Season to taste with more salt and pepper.

Using a small spoon and your fingers, fill the hollowed potatoes with this mixture; it should mound a bit. Sprinkle on the cheese.

Return the potatoes to the 450 degrees F oven and bake until the filling heats through, 8 to 10 minutes. Sprinkle with the remaining chives and serve warm.

Make Ahead: You can stuff the potatoes up to two days ahead as long as you wrap them in plastic wrap and refrigerate them; bring them to room temperature before the second baking.