Heat olive oil in an 8 quart stock pot on medium-low heat. Add onions and cook until tender and translucent without letting the onions brown, about 45 minutes.
Add flour and let cook until the flour flavor comes out, about five minutes. Deglaze the pan by adding the cold red wine. Scrape up any stuck, brown bits.
Add beef broth and dark balsamic vinegar. Season with salt and pepper, and simmer for 30 minutes.
Turn broiler on low and ladle soup into over safe ramekins. Top bowls with one slice of baguette and evenly divide cheese among bowls. Place bowls on cookie sheet and broil in the preheated oven until cheese bubbles and browns slightly, about 5-6 minutes. Serve and enjoy!