Heat oil in a large pan. Add onions and saute until soft.
Stir in chicken, beans, salsa, tomatoes, chili peppers, chili powder, lime juice, red pepper flakes, salt & pepper. Bring to boil, reduce heat and cook for 15 minutes.
Meanwhile spray a large baking sheet with cooking spray and preheat oven to 350 degrees. Place 3/4 cup enchilada mixture in the center of each tortilla. Fold up the sides of the tortilla around the filling & then fold up the ends to enclose the filling; place seam-side down. Top each tortilla with 1/4 cup of cheese.