Place the chicken in the slow cooker and add 3/4 cup of the salsa, the cream cheese, sliced jalapeño, salt, and pepper; stir to combine.
Cover and cook on high until the chicken is cooked through and tender, about 6 hours.
Remove the chicken and shred it with two forks, then return shredded chicken to the slow cooker and stir in the remaining 1/4 cup salsa.
Spoon an even amount of the shredded chicken mixture onto each tortilla, sprinkle with the grated cheese, and roll tightly to form flautas.
Heat a large dry nonstick skillet over low–medium heat. Place the rolled flautas seam-side down in the skillet and cook, turning occasionally, until all sides are lightly browned and crisp.
Transfer to a plate and serve warm.
Notes
Use mild salsa to control heat from the jalapeño.
Shred chicken while still warm for easier shredding.
Cook flautas over low–medium heat to brown without burning.
Keep a close eye while crisping since no oil is used.