In Dutch oven, mix squash, apple, onion, brown sugar, salt, cinnamon and pepper. Add broth. Cover; heat to boiling over medium-high heat. Reduce heat; simmer about 20 minutes or until squash is tender.
In blender or food processor, place one-third of mixture. Cover; blend until smooth. Repeat twice to use up remaining soup. Return to Dutch oven, stir in milk and yogurt. Heat over low heat, stirring occasionally, just until heated through. Ladle into bowls; sprinkle with chives.