In a small bowl mix together the all purpose flour, garlic powder, onion powder, salt and pepper. Add the chicken breasts to a bowl and sprinkle over the flour-spice mixture and toss to coat all of the chicken breasts well. Set aside.
In a large oven-safe skillet, add the butter over medium heat. When the butter is melted, add the sliced yellow onions, pinch of sugar and 1/2 tsp salt. Stir to combine and cover and cook for 5 minutes, undisturbed. Then remove the lid and turn to medium-low heat. Cook the onions, stirring occasionally (so they don't burn), until golden brown and caramelized, about 20-30 minutes.
While the onions are cooking, preheat the oven to 400F.
When the onions are caramelized, stir in the dried thyme, tamari, minced garlic and ground pepper. Stir to combine and then transfer the onions to a bowl.
Turn the large skillet to medium-high heat and add 1 tbsp olive oil. When the oil is hot, add the seasoned chicken breasts to the pan and cook undisturbed until browned, about 4-5 minutes. Flip the chicken and repeat on the other side, 4-5 minutes. Remove the chicken from the pan.
Put the pan back on medium heat and add the caramelized onion mixture back to the pan. In a medium mixing bowl whisk together the hot water with the bone broth concentrate and cornstarch and then pour that mixture into the pan. Scrape up any browned bits from the bottom of the pan and mix everything in the pan together to combine. Let simmer for 2-3 minutes until the sauce starts to slightly thicken.
Nestle the chicken breasts into the sauce and spoon some of the sauce and onions over each chicken breast. Then, divide the grated cheese over top all of the chicken breasts. Bake uncovered in the preheated oven for 15-20 minutes, until the chicken registers 165°F on an instant read thermometer and the cheese is melted.
Garnish the tops of the chicken breasts with fresh thyme leaves and serve immediately.