Pour red wine vinegar, 2 Tablespoons olive oil, garlic, thyme, and sea salt into a large reusable plastic bag. Add chicken breasts and massage mixture over the chicken using your hands. Set aside.
To a large baking dish, add sliced apple, Brussels sprouts and sweet potato. Drizzle medley with 2 Tablespoons of olive oil.
Place chicken over the fruit and vegetable medley and bake in a preheated oven for about 30 minutes (chicken should be 165 degrees Fahrenheit in the center).