To a large soup pot over medium-high heat add turkey, the peeled chopped apple, and shallots. Season with salt and pepper then cook until turkey is no longer pink, breaking it up as it cooks. Add garlic then cook for 1 more minute. Add chopped chipotle chilies and sauce, chili powder, and cumin then stir and cook for 1 more minute.
Add tomato sauce, chicken broth, apple cider, bay leaf, and cinnamon stick to the pot then turn heat up to high and bring chili to a boil. Reduce heat to medium then cook for 10 more minutes. Scoop into bowls then top with shredded cheddar cheese and crushed tortilla chips. Chop remaining apple (do not peel) then sprinkle on top.