Place the 13 ounces of boneless and skinless chicken breasts in your slow cooker.
Pour in 3/4 cup of the mild salsa over the chicken, ensuring it's well coated.
Sprinkle the 1/4 teaspoon salt and 1/8 teaspoon pepper over the chicken for added flavor.
Dollop the 1/4 cup of low-fat cream cheese on top of the chicken, and add the sliced jalapenos.
Cover and cook on low for 6-7 hours or on high for 3-4 hours, until the chicken is tender and easily shredded.
Once cooked, remove the chicken from the slow cooker and shred it using two forks. Return the shredded chicken to the slow cooker and mix with the remaining 1/4 cup salsa.
Preheat your oven to 400°F (200°C). Lay out the whole-grain tortillas and spoon a generous amount of the chicken mixture onto one side. Sprinkle with 1/2 cup low-fat cheese, then roll up tightly.
Place the rolled flautas seam-side down on a baking sheet. Bake for about 15-20 minutes, or until they are golden brown and crispy.
Remove from the oven and let cool slightly before serving. Enjoy your Slow Cooker Jalapeno Chicken Flautas with your favorite toppings like guacamole, sour cream, or additional salsa!