In a large resealable container, combine the red wine, carrots, onions, celery, thyme, garlic and bay leaves. Add the chicken thighs, seal the container and marinate in the refrigerator overnight.
When ready to cook, preheat the oven to 400 degrees F.
Toss the mushrooms with the olive oil on a baking sheet and roast until brown, 10 to 15 minutes. Set aside.
Drain the chicken and vegetables thoroughly in a colander, reserving the wine mixture. Pat the chicken dry with a paper towel (reserve the vegetables and aromatics). Season the chicken with salt and pepper and transfer to a clean bowl. Add the flour and toss until thoroughly coated.
In a large Dutch oven, heat the canola oil over medium-low heat. Add the bacon and cook, stirring often, until caramelized and the bacon has released its fat, 5 to 8 minutes. Set the lardons aside. Turn the heat up to medium high and shake the excess flour off the chicken. Brown the chicken on all sides, 2 to 3 minutes per side. Remove the chicken and set aside.
Add the pearl onions and drained vegetables and aromatics to the same pot and cook over medium heat until caramelized, 8 to 10 minutes. Add the reserved red wine mixture and cook until reduced by half, 10 to 15 minutes. Add the chicken stock and bring to a simmer. Season with salt and pepper. Return the chicken to the pot and cover.
Transfer to the oven and cook until the chicken is tender and the sauce has thickened, 30 to 40 minutes. If necessary, finish the dish on the stove by simmering it uncovered to reduce the mixture further, depending on how thick you'd like the sauce.
Serve with buttered egg noodles on the side and chopped parsley. Garnish with the reserved lardons and mushrooms.