Heat butter in a large pot over medium heat; cook and stir onion in the melted butter until translucent, 5 to 10 minutes. Add butternut squash, potatoes, apple, carrot, and celery to onion; pour in chicken broth and enough apple cider to cover vegetables. Bring mixture to a boil and cover pot. Reduce heat and simmer, adding more apple cider as needed, until vegetables are tender, 35 to 40 minutes.
Blend vegetable mixture with an immersion blender until smooth; stir in cream, cinnamon, and cloves. Simmer until heated through, 5 to 10 minutes. Spoon soup into serving bowls; top each with about 1 tablespoon sour cream and a pinch of nutmeg.