Prick potatoes with a fork. Bake for 1 hour at 425 degrees F. Let cool slightly.
Cut potatoes in half lengthwise; scoop out pulp for other desired use, leaving a 1/2-inch shell. Place potato shells on a baking sheet; spray inside of shells with cooking spray. Bake at 425 degrees F for 15 minutes or until crisp.
Combine chicken, 1 cup cheese, chipotle pepper and liquid, taco seasoning, and sour cream; divide evenly among potato shells. Bake at 425 degrees F for 5 minutes. Top with remaining cheese and bake an additional 5 minutes or until cheese melts. Sprinkle with chives.