How to Make It
Preheat the oven to 350°. Place the squash, cut side down, on a baking sheet and bake until tender, about 40 minutes. Let cool slightly. Using a spoon, scoop out and discard the seeds. Scrape the squash from the skin.
Meanwhile, in a large heavy saucepan or flameproof casserole, melt the butter over low heat. Add the leeks and thyme and cook, stirring occasionally, until soft and browned, about 40 minutes. Discard the thyme sprigs.
Stir in the stock and the squash. Simmer over moderate heat for 20 minutes. In a blender or food processor, puree the soup in batches until smooth. Pour the soup back into the pan and season with the salt and pepper.
To serve, ladle the soup into bowls and garnish each serving with 1 tablespoon sour cream, 1 teaspoon chives and a sprinkling of the bacon.
Make Ahead: The recipe can be prepared through Step Three up to 2 days ahead. Reheat the soup before proceeding.