To a slow cooker, add the onions, thyme, red wine, butter, soya sauce, balsamic vinegar, brown sugar,flour and pepper.. Set the temperature to high, and cook for 5 hours.
Open the slow cooker and stir everything together. Pour in the 6 cups of beef broth, stir everything together. Warm through for 5 minutes to bring up to temperature.
Ladle some soup into bowls. Top with the toasted baguette, sprinkle cheese over the top. Place the soup bowls on a baking sheet.
Turn the broiler to low, broil the soup for 5-6 minutes until the cheese is melted and golden brown.