Melt the butter in a large pot over medium heat. Stir in the onion, ginger, and jalapeno pepper; cook and stir until the onion has softened and turned translucent, about 7 minutes. Add the butternut squash and chicken broth, and bring to a boil over high heat. Reduce heat to medium-low, cover, and simmer until the squash is tender, about 30 minutes.
Stir in the evaporated milk, coconut milk, sugar, salt and pepper. Cook and stir 5 minutes more.
Using a stick blender, puree the soup right in the cooking pot. Ladle into bowls, and garnish with sour cream and thyme to serve. (If you don't have a stick blender, a regular blender works just fine but takes a bit more time.).