In a bowl, add chicken and all of the marinade ingredients. Cover and refrigerate for 12 hours or up to overnight.
Remove the chicken, onions, and carrots from the marinade. Pat them dry with paper towels. Set them aside.
Strain the wine marinade, skim off the scum, and discard the spices. Simmer it in a saucepan over medium heat until it's reduced in half. Set it aside.
Preheat the oven to 250°F.
In a Dutch oven, heat 1 tablespoon of oil over medium-low heat. Cook bacon until crispy. Transfer to a plate.
Working in batches, brown the chicken in bacon grease over medium heat for 3 minutes on each side. Transfer to a plate.
Add the marinated onions and carrots (from step #2). Cook for 6 minutes, stirring often. Cook garlic for 1 minute.
Add brandy and scrape the brown bits from the bottom of the pan. Cook until the liquid is reduced in half.
Add the marinade sauce (from step #3), chicken, broth, half of the crispy bacon, (7) thyme sprigs, and (1) bay leaf. Bring it to a simmer then turn off the heat.
Cover the pot, and put it in the oven. Cook for 30 minutes or longer until the chicken is fully cooked.
While waiting for the chicken to cook, heat oil and butter in a skillet over medium-high heat. Add pearl onions, a pinch of salt, and a pinch of sugar. Cover the pan and cook on low heat until caramelized, about 10 minutes. Shake the pan occasionally. Transfer them to a plate.
Add mushrooms and cook for 5 minutes. Add half of the crispy bacon, stir for 1 minute, then set them aside.
Remove the pot from the oven. Transfer the chicken and vegetables to a plate.
Strain the sauce and discard the spices. Bring the sauce to a simmer over medium heat. Whisk a mixture of softened butter and flour (Beurre Manie) into the sauce. Simmer for 7 minutes, stirring often.
Add cooked chicken and vegetables back into the pot. Simmer for 10 minutes.
Add mushrooms, pearl onions, and crispy bacon. Bring it to a boil then turn off the heat immediately and serve.