To a medium bowl, add blackberry preserves, olive oil, soy sauce, apple cider vinegar, Dijon mustard, garlic, salt, pepper, and red pepper flakes. Mix until fully incorporated and set aside.
Pat chicken dry with paper towels.
In a small bowl, combine salt, pepper, and chili powder. Sprinkle the seasoning mixture evenly over the chicken thighs.
To a large nonstick skillet over medium heat, add olive oil. Once hot, add chicken thighs. (Depending on the size of your skillet, you may need to work in batches.) Cook chicken for 5 minutes, then flip and reduce the heat to medium-low. Continue cooking for another 5 minutes, or until the internal temperature reaches 165°F. Remove chicken from the skillet and transfer to a plate. Tent loosely with foil to keep warm.
Raise the heat to medium. To the same skillet, add sliced jalapeño pepper and cook for 3 minutes, stirring occasionally. Add blackberries to the skillet and cook for another 3 minutes, gently pressing some of the berries with the back of a spoon to release their juices, while leaving others whole for texture.
Pour the blackberry glaze into the skillet with the blackberries and jalapeños. Stir to coat everything evenly and let simmer for 1 to 2 minutes until slightly thickened.
Return the chicken to the skillet. Spoon glaze over the top, and cook for 1 to 2 minutes more, or until the chicken is warmed through and well coated in the glaze.
Serve warm.