In a large, heavy pot over medium heat, bring 2 quarts water to a boil. Stir in bouillon cubes and let boil 10 minutes, until dissolved. Place onions in boiling water, reduce heat and simmer 30 minutes.

Stir in salt and pepper and simmer 30 minutes more.

Stir the flour into 1/2 cup cold water to make a paste. Gently whisk this mixture into the simmering soup, being careful not to break the onions. Simmer 30 minutes more.

Stir in cream and cheese until cheese is melted and mixture is thoroughly heated. Thin with water if necessary. Serve hot, garnished with croutons, if desired.