Bake potatoes, wrapped in foil until fork tender. Cool at room temperature for an hour or so. Slice potatoes lengthwise and scoop out the insides into a large bowl, leaving at least 1/4 inch of potato in the skins. Place skins on a baking sheet to use later.
Add sour cream, soup, bacon and more than half of the cheese to potatoes in a bowl. Whip with electric mixer until barely blended. Fold in chives and bacon. Scoop mixture back into the potato shells and top with rest of cheese. Bake in oven at 375 until bubbly and browned.