In a skillet, saute onion and garlic in oil until tender. Add squash and saute until tender. Add chicken and chilies; heat through.
In a saucepan, melt butter. Add flour, chili powder, salt and pepper; stir to form a smooth paste. Gradually add milk, stirring constantly. Cook until sauce comes to a boil; cook an additional minute until thickened. Add 1/3 cup sauce to chicken mixture; mix well. Place 1/3 to 1/2 cup chicken mixture down the center of each tortilla; top with 1 tablespoon cheese. Roll up and place seam side down in a greased 13x9-in. baking dish. Spread remaining sauce on top.
Cover and bake at 400° for 25 minutes. Uncover; sprinkle with tomatoes and remaining cheese. Return to the oven for 5 minutes. Serve with sour cream.