Pat chicken dry with paper towels and brown on all sides. Season chicken with salt and pepper to taste, reduce heat to medium-low, return bacon to Dutch oven, cover and slowly cook for 10 minutes, turning chicken every 2 minutes or so. Uncover, pour cognac over chicken and cook off alcohol by carefully lighting it with a flame. When flame is out, add wine and just enough chicken stock to cover chicken. Stir in tomato paste, garlic and herbs. Bring to a simmer, cover and slowly simmer 25 to 30 minutes.
While chicken is cooking, prepare onions and mushrooms. In a large sauté pan over high heat, melt remaining 2 tablespoons butter. Add onions and cook for 10 to 15 minutes. Add mushrooms and cook an additional 5 to 8 minutes. Season with salt and pepper and reserve.
When chicken is tender (and juices run clear yellow when meat is pricked with a fork), remove chicken from Dutch oven. Return pot to stove and simmer chicken cooking liquid for 1 to 2 minutes, skimming off fat. Increase heat to high and boil rapidly to reduce liquid to about 2 1/4 cups. Adjust seasonings. Remove from heat and discard bay leaf.
In a small bowl, whisk together flour and butter into a smooth paste. Whisk paste into hot liquid, return pot to stove over medium heat and simmer, stirring, for 1 to 2 minutes. Sauce should be thick enough to lightly coat a spoon. Place chicken and onion-mushroom mixture back into Dutch oven and serve.