Preheat oven to 400 degrees F (200 degrees C). Bake potatoes for 1 hour, or until done. Potatos can be cooked in the microwave or left over baked potatos can be used as well. Set aside to cool.
Melt butter in a 3 quart saucepan over medium heat. Saute onions until tender and golden brown. Stir in flour, and cook 5 minutes to make a roux. Pour in chicken stock and water. Add cornstarch and mashed potato flakes. Season with salt, pepper, hotsauce and thyme. Bring to a boil, reduce heat, and simmer for 5 minutes.
Remove the skin from the cooled potatoes, and discard. Dice the potatoes into 1/2 inch cubes, and stir into soup, along with the half-and-half. Simmer for 15 to 20 minutes, or until thick. Spoon into bowls, and garnish with shredded cheese, bacon and chopped green onion.