Add the chicken, salsa and taco seasoning to a slow cooker. Cook on low for 4 hours. Shred the chicken using two forks and mix with the juices in the slow cooker. Keep warm.
Spread a tablespoon of chipotle sauce onto the center of top of each flour tortillas. Top with some shredded chicken and cheese. Fold both of the sides over to the middle and fold the bottom up over the top to form an envelope.
Grease a non-stick skillet with cooking spray and heat to medium heat. Add the quesadillas and cook in batches until browned on the bottom, flip until browned on the other side.