Preheat oven to 425 degrees. In a medium bowl, combine chicken and scallions. Season generously with salt and pepper; set aside.
In a blender, puree pumpkin, garlic, jalapeno, chili powder, 2 1/2 cups water, 2 teaspoons salt, and 1/4 teaspoon pepper until smooth (hold top firmly as blender will be quite full). Pour 1 cup of sauce in the bottom of an 8-inch square (or other shallow 2-quart) baking dish.
Lay tortillas on work surface; mound chicken mixture on half of each tortilla, dividing evenly. Roll up tortillas; place, seam side down, in baking dish.
Pour remaining sauce on top; sprinkle with cheese. Place dish on a baking sheet; bake until cheese is golden and sauce is bubbling, 25 to 30 minutes. Let cool 5 minutes before serving.