Heat 1 tablespoon olive oil in a large soup pot over medium heat. Add onion, season with Kosher salt, and cook until softened, stirring occasionally, for 5-7 minutes. Add roasted squash, roasted apple, thyme, and vegetable stock. Season with Kosher salt to taste. Bring mixture to a boil, then reduce heat and simmer for 20-30 minutes.
Place soup in a blender, working in batches, and blend until soup is smooth and creamy.
Meanwhile, in a small bowl, combine creme fraiche, apple cider vinegar, and a pinch of cayenne pepper. Add a pinch of Kosher salt.
Ladle soup into individual bowls and add a swirl or dollop of the creme fraiche mixture on top. Sprinkle with pecans and enjoy!