Heat oil in a large soup pot over medium heat.
Add onions, garlic, and peppers.
Cook until vegetables are soft, approximately 5 minutes.
Add in chili powder, cumin, and red pepper flakes and stir.
Add chicken broth, tomatoes, and refried beans and stir well.
Bring to a boil, then reduce heat to a simmer.
Add corn, butternut squash, and chicken.
Cover and cook until chicken is cooked thoroughly, approximately 10 minutes depending on the thickness of the chicken breast.
When chicken is done, remove it from the pot and place it on a plate.
Using two forks, shred the chicken.
Add the shredded chicken back to the pot.
Add in lime zest, stir well.
Add additional red pepper flakes if desired.
Let simmer until ready to serve.
Serve with a dollop of nonfat greek (or plain) yogurt and chopped fresh cilantro.