Preheat oven to 300F. Season beef cubes all over with salt and pepper. Heat a Dutch oven (or a large oven-safe high-walled skillet) over medium-high heat, then add olive oil. Sear beef cubes 2-3 minutes on all sides until a deep golden brown.
Add onion to pot and saute an additional 2-3 minutes until slightly softened. Add chipotle and garlic and saute 1 additional minute until fragrant. Pour red wine into pot and bring to a simmer. Reduce heat to medium and allow to simmer 5 minutes until reduced in half.
Add thyme, bay leaf, and beef broth to pot, stir well, and bring to a simmer over medium heat.
Remove Dutch oven from heat, cover, and place in 300F oven and let cook 45 minutes. Remove from oven and add potatoes and butternut squash. Return to oven and continue cooking an additional 30-45 minutes or until chuck roast and vegetables are very tender. Discard bay leaf and thyme sprigs.
Spoon a bit of the broth into a small bowl. Add flour and whisk until smooth. Add back to stew, folding until combined.
Ladle stew into bowls and serve with crusty bread if desired. Enjoy!