Cut the butternut squash in half and scoop out the seeds. Place both halves, cut side down in a microwave-safe dish and add a quarter inch of water to the dish. Cover with plastic wrap and cook in the microwave for 10-15 minutes or until it can be easily pierced with a fork. Scoop out the squash and set aside.
Fry onions and garlic in butter in a large pot. Stir in chicken broth, apple juice, butternut squash puree and pumpkin puree. Bring to a boil over medium heat, stirring occasionally. Turn the heat to low and simmer for 10 minutes, stirring often. Stir in nutmeg, pepper, and salt.
Carefully pour the soup into a blender or food processor and blend until smooth. This step can be done in batches, if necessary.
Garnish with sour cream and roasted seeds.