Stir apple cider, honey, cider vinegar, and brown sugar in a saucepan over medium heat. Bring to a simmer and reduce heat to low, stirring often, until the mixture reduces to 2/3 cup, about 20 minutes.
Simmer 1/3 cup whiskey in a separate small saucepan over medium-low heat until steam no longer smells of alcohol, about 10 minutes; stir into the apple cider mixture. Reduce this mixture to 1/2 cup, forming an apple cider glaze and cool.
Stir 3 tablespoons whiskey into apple cider glaze.
Preheat oven to 350 degrees F (175 degrees C).
Place pork chops into a baking dish; brush with the apple cider glaze.
Bake chops in the preheated oven, basting them often with glaze, until tender, about 1 hour. If desired, bring any remaining glaze to a boil in a saucepan and drizzle over chops to serve.