preheat oven to 350°. Cook jumbo shells according to package directions. Drain. Rinse with cold water and drain again.
In a large skillet cook sweet peppers, red onions, and jalapeno pepper in hot oil over medium heat about five minutes or until tender. Stir in chicken, 1/2 cup of the enchilada sauce, the refried beans, taco seasoning mix, and 1/4 teaspoons salt. Cook and stir for five minutes. Stir in 1/2 cup of the cheese and 1/2 cup of the green onions.
Spread 1 cup of the remaining enchilada sauce in the bottom of a 3 quart rectangle or baking dish. Sprinkle 1 cup of chips over enchilada sauce. Spoon chicken mixture into cooked shell. Arrange the shells in the baking dish. Drizzle with the remaining enchilada sauce.
Bake, covered, for 30 minutes. Sprinkle with remaining 1/2 cup cheese, cook uncovered, about five minutes or until or until cheese is melted. Sprinkle with remaining green onions and remaining nacho chips. Serve with sour cream.