Heat the olive oil in a large Dutch oven over medium heat. Cook the bacon until crisp, then remove with a slotted spoon.
Season the chicken with salt and pepper and brown it in the bacon fat in batches until golden on all sides. Set aside.
Add the carrots, onion and garlic and cook until the onion is soft, about 5 minutes.
Return the chicken and bacon to the pot. Add the Cognac and carefully ignite it with a long match. When the flames die down, add the wine, stock and thyme.
Bring to a simmer, cover and transfer to the oven. Cook about 1 hour, until the chicken is tender.
Meanwhile, melt 1 tablespoon butter in a skillet and brown the frozen onions until cooked through. Set aside. Melt the remaining butter and sauté the mushrooms until browned.
Transfer the chicken and vegetables to a serving dish and discard the thyme.
Set the Dutch oven over medium heat, stir the flour into the liquid and cook, stirring, until thickened, about 5 minutes.
Add the onions and mushrooms, heat through and pour the sauce over the chicken.
Notes
A Burgundy or Pinot Noir works well. The dish can be made a day ahead and reheated gently.