Melt butter in large pot over medium-high heat. Add onion and nutmeg; sauté until onion begins to brown, about 5 minutes. Add squash, 4 1/4 cups broth, apple, and apple juice. Bring to boil; reduce heat and simmer uncovered until squash and apple are tender, about 30 minutes.
Working in batches, puree soup in blender until smooth. Return soup to pot. Season to taste with salt and pepper. Bring soup to simmer, thinning with more broth if desired. Ladle soup into bowls.
Garnish with sour cream and chives.