Preheat oven to 475F and adjust the rack to the middle position. Sprinkle each chicken thigh with sea salt. Place 1 tablespoon of the ghee in a 12” oven-proof skillet over medium high heat, swirling the pan to coat. Place the chicken skin-side down in the skillet and cook until the skin is browned and crisp, about 8 minutes. Flip the chicken pieces and continue to cook until browned on the second side, about 5 minutes. Transfer chicken to a plate.
Reduce the stove temperature to medium and add the remaining 1 tablespoon ghee, shallot and garlic and cook until fragrant, about 45 seconds. Sprinkle the coconut flour over the garlic mixture, stirring constantly and cook for about 1 minute. Slowly stir in the broth, sea salt and lemon juice, scraping the bottom of the pan to release any browned bits. Bring to a simmer. Stir in the zest and remove from the heat. Place the chicken, skin-side up, in the pan with the garlic mixture and place in the oven. Roast for about 10 minutes until chicken is cooked through.
Let chicken rest for 5 minutes, sprinkle with parley and thyme. Season to taste with sea salt and serve.