In a large soup pot, add your butter and allow it to melt over medium-low heat. Next, add the thinly sliced onions and bay leaves. Sauté over medium-low heat until onions begin to turn a golden-brown color.
When onions are sautéed, sprinkle thyme into the pot, then sprinkle all-purpose flour over the onions. Stir until the onions are completely coated in flour. Continue cooking for about three minutes.
Next, add red wine and balsamic vinegar to the pot. Cook over medium-low heat until the wine has completely evaporated, stirring occasionally.
When the wine has completely evaporated, add your beef broth to the pot. Stir so that everything is mixed. Allow the soup to simmer while covered on low heat until shortly before you are ready to serve.
Right before you’re ready to serve, dish the soup into your serving dishes. Add slices of baguette to the top of your soup, then sprinkle shredded cheese on top. Place it into the oven on a low broil. Broil for about five minutes, or until the cheese has turned a golden brown and has melted. Please note that the amount of time on broil may vary depending upon your specific oven. Be sure to keep a close eye on it so that your soup does not burn.