Combine the flour, salt, and pepper on a large plate. Dredge the chicken pieces in the flour. In a large Dutch oven (with a lid), heat 2 tablespoons of the olive oil. Brown the chicken pieces until golden brown on all sides. Remove the chicken pieces and set aside. Wipe the pan clean with a paper towel. In the same pot, heat the remaining 1 tablespoon olive oil, add the pearl onions and saute until golden brown. Add the mushrooms and ham and saute for 2 minutes. Add the garlic and, when fragrant, add the brandy and thyme and reduce for 2 minutes. Add the red wine, stock, tomato paste, and bay leaves. Bring to a simmer and add the chicken pieces. Cover and cook slowly for about 35 minutes, or until chicken meat comes off the bone easily. Remove the bay leaves. Adjust the seasoning with salt and pepper to taste. Sprinkle with chopped parsley. Serve with mashed potatoes or egg noodles.