Wash the tomatoes, peel the garlic and onion, and cut the onion into quarters. Put them in a small saucepan, cover with water and boil for about 10 minutes.
Put the tomatoes, garlic, onions, and 2 cups of their cooking water into a blender. Add the paprika, chili powder, chipotle peppers and adobo sauce. (If you are heat averse, add less chipotle and adobo.) Blend until smooth.
Shock the sauce. Place a stockpot over medium high heat and add 2 T olive oil. When the oil is hot, pour in the tomato mixture. Stir and simmer for 10 minutes until the sauce thickens a bit and the oil is incorporated.
Turn the heat to high and add the cubed sweet potatoes, the stock, and the cider vinegar. Bring to a boil, then turn down to medium-low. Cover and cook for 12-15 minutes until the sweet potatoes are soft.
Transfer the sweet potatoes and a cup or so of the broth to a blender, Add the flour and blend until smooth. Return the blended sweet potato mixture to the stock pot and salt and pepper to taste. Simmer for 10 minutes until the soup is creamy. Add the cheese and continue to simmer until the cheese melts.