In a dutch oven over medium-low heat, add onions, butter, salt and pepper. Cook for 45 minutes, stirring occasionally until onions are a deep brown. Stir in some fresh thyme leaves and flour.. Deglaze the pan with chicken stock and stir until thickened.
While onions are cooking, add chicken to a baking dish. Drizzle with olive oil and cover with aluminum foil. Bake for 25-30 minutes or until cooked through.
Add chicken to the pan with caramelised onions. Spoon some onions on top of the chicken. Add the sliced swiss on top of the chicken. Cover the dutch oven until cheese is melted. Serve and enjoy!