1. Melt butter in a Dutch oven or large sauce pan over medium heat. Add carrot, onion, celery, red bell pepper and garlic; cook until tender, about 8 minutes. Add pepper flakes and squash and cook until tender, about 10 minutes.
2. Add chicken broth and mix well. Bring to a simmer. Add crab meat; cook over low heat until thoroughly heated.
3. Whisk together flour and a little of the milk to make a paste. Add remaining milk and mix well. Add to soup.
4. Cook, stirring, until soup thickens, about 10 minutes. Do not boil. Garnish with chives to serve.