Add the chili powder, cumin, salt and pepper. Stir until onion and garlic are well-coated.
Add the tomatoes, pumpkin, coconut sugar and vinegar to the sauce and stir until well-combined. Bring to a boil, then turn the heat to low and cover. Allow sauce to simmer for ~15 minutes.
In a large bowl combine the shredded chicken, greek yogurt, pumpkin and green chilies. Stir until all ingredients are combined and chicken is coated with sauce. Season with cumin, salt, pepper and nutmeg.
When the sauce is ready, add a thin layer of sauce to the pan. Divide the chicken mixture evenly among 10 corn tortillas.
Roll each tortilla and place in the pan seam-side down. Top the enchiladas with remaining sauce and sprinkle with cheese.
Bake at 350F for 15 minutes, or until cheese is melted and enchiladas are warmed through. Garnish with cilantro and serve immediately.