Heat oven to 375°F, and spray a 13 x 9-inch baking dish with nonstick spray.
Heat a large skillet over medium heat. Add butter. Add onion, bell pepper and jalapeno pepper and cook, stirring often, until onion is translucent and peppers are tender. Add minced garlic, stir, and cook 30 seconds. Stir in chili powder, cumin, red pepper flakes, salt and black pepper; cook, stirring occasionally, 1 minute.
Sprinkle the flour over the vegetable mixture and cook, stirring constantly, 1 minute.
Add the broth and lime juice and whisk. Increase heat to high and bring mixture to a boil, stirring constantly. Boil 1-2 minutes, stirring occasionally, or until thickened. Remove from heat and stir in green chile tomatoes and sour cream.
In a large bowl, combine chicken and cilantro; add vegetable mixture and mix well.
In a medium bowl, mix together both cheeses.
Line the prepared casserole dish with 1/3 of the semi-crushed tortilla chips. Top with ½ the chicken mixture and 1/3rd of the cheese. Repeat the layers once with the last two layers being tostito chips and cheese.
Spray a large sheet of aluminum foil with nonstick spray to loosely cover the casserole dish.
Bake at 375°F for 30 minutes. Uncover and bake another 10-15 minutes or until lightly browned and bubbly. Let stand 10 minutes before serving.
Top with garnishes of your choice.
Enjoy!