Melt butter in large saucepan over medium heat. Add onions and thyme, season with pepper. Cover and cook until onions are translucent, stirring occasionally, about 15 minutes. Cook until they are brown and caramelized, another 10 minutes.
Add flour to onions and stir until browned, scraping bottom of pan for about 5 minutes. Mix in water, wine, soy sauce, and honey. Bring to boil. Reduce heat; cover and simmer until soup is slightly thickened, about 1 1/2 hours. Add shredded Swiss cheese, stir till melted. Serve with French bread.