Add the sliced onions and sauté until the onions are lightly browned. Add the garlic and carrots and cook for another 2 minutes. Add the thyme, bay leaf and rosemary. Pour in ½ cup of the brandy and deglaze the pan by scraping up any brown bits on the bottom of the pot. Pour in the red wine, chicken stock, and diced tomatoes and bring the mixture to a simmer. Return the chicken and any juices on the plate to the pot. Cover with a tight-fitting lid and transfer the pot to the oven for 30 to 40 minutes, until chicken is cooked through.
Mix the remaining 3 tablespoons of the butter with the flour, making a paste (called a beurre manié). When chicken is tender, remove the pot from the oven and place it on the stovetop. Transfer the chicken pieces to a deep serving vessel. Stir the beurre manié into the braising liquid and simmer until the sauce starts to thicken. Add the sautéed pearl onions and mushrooms and season to taste with salt and pepper. Pour the vegetables and sauce over the chicken in the serving vessel, sprinkle with the fresh thyme and cooked bacon and serve.
Tip – To making peeling fresh pearl onions easier, trim the root and stem. Blanch them in boiling water for a couple of minutes before peeling.