Dry chicken thighs with paper towels. Season with salt and pepper on both sides. Rub a pinch of smoked paprika onto the skin side.
In a large frying pan, sauté pan, or wide Dutch oven, cook bacon over medium high heat until crisp. Remove the bacon from pan with a slotted spoon and drain on paper towels. Set aside.
Drain all but 2 tablespoons of drippings from the pan. Brown the chicken over medium-high heat, starting with the skin side down, for 3-4 minutes per side, until golden. Depending on the size of your pan, you might have to do this in 2 batches. Transfer chicken to a plate and set aside.
Pour off all but 2 tablespoons of fat from the pan. Add apple wedges and shallots, and sauté over medium-high heat until apples are just beginning to brown around the edges, about 4-5 minutes. Add garlic and cook until fragrant, 1 minute.
Stir in flour and cook for 1-2 minutes. Pour in hard cider and chicken broth, scraping the brown bits from the bottom of the pan. Stir in Dijon and grainy mustards, all but 2 tablespoons of the reserved bacon, 1/2 teaspoon kosher salt, and 1/2 teaspoon black pepper.
Add the chicken and any accumulated chicken juices back to the pan, skin side up. Nestle the chicken thighs into the apples and sauce, but don't fully submerge them. Bake for 20-25 minutes, until the sauce is bubbling and the chicken registers 170-175 degrees F away from the bone.
Remove chicken and apples from the pan to a platter and loosely tent with foil. Return the pan to the stove to finish the sauce.
Use a spoon to skim any extra fat from the top of the sauce. Stir in heavy cream and Applejack (if using) into the sauce and simmer for 2-3 minutes. Season to taste with salt and pepper.
Spoon the sauce over the chicken and apples and serve with egg noodles or potatoes. Garnish with the reserved bacon.