In a saucepan, heat the olive oil over medium heat. Add the onion, garlic and thyme and cook for 10 minutes. Add the tomatoes, chicken broth and chipotle; lower the heat and simmer for 15 minutes.
Using a blender, puree the soup.
Butter 1 side of each bread slice. Spread the unbuttered side of 18 slices with mustard; top with a slice of cheese and the remaining bread slices, buttered side up. In a nonstick skillet or griddle, grill the sandwiches over medium heat until the cheese is melted, 3 to 4 minutes on each side. Serve with the soup.