In a large, heavy, flameproof casserole over medium heat, melt 1 tablespoon of the butter. Add the bacon and cook until light golden, about 10 minutes. Remove with a slotted spoon and set aside.

Increase the heat to medium high and arrange the chicken thighs, skin side down, in a single layer with space between them. (You may have to do this in two batches.) Season with salt and pepper and cook until light golden, about 5 minutes per side. Remove the chicken and pour off all but 1 tablespoon of the fat from the pan. Turn the heat to medium, add the chopped onion, and cook until soft, about 5 minutes.

Increase the heat to medium high. Return the chicken and bacon to the pan. Add the wine, broth, tomato paste, bay leaves, and thyme. Bring to a boil, reduce the heat to low, cover, and simmer until the chicken is cooked through, about 15 minutes.

Remove the chicken from the pan, cover with foil, and set aside. Add the parsnips, carrots, Brussels sprouts, and pearl onions (if using), to the stock. Cover and cook until the vegetables are tender, 10 to 15 minutes. With a slotted spoon, remove the vegetables from the pan. Turn the heat to high and reduce the broth until 2-1/2 to 3 cups remain, about 15 minutes.

In a small bowl, mash together the flour and the remaining 1 tablespoon butter with a fork to make a paste. Bring the liquid to a boil. Whisk the flour and butter paste into the broth, simmering until the liquid thickens slightly and coats a spoon, 2 to 3 minutes.

To serve, heat the sauce over medium-high heat until it's just simmering. Add the chicken and the vegetables and heat thoroughly for a few minutes. Serve the chicken and vegetables with plenty of the sauce and garnish with the parsley.