Brown the beef. Pat the beef dry and season with salt and pepper. Heat 1 tablespoon oil in a large Dutch oven over medium-high heat. Working in batches, sear the beef until deeply browned on all sides. Transfer to a plate.
Build the base. Add the remaining oil and the onion to the pot. Cook for 4–5 minutes until softened. Add the tomato paste and cook for another 3-4 minutes. Then add the garlic for 1 minute.
Deglaze with wine. Pour in the red wine, scraping up the browned bits from the bottom of the pot. Let it simmer for 2–3 minutes until reduced.
Add the broth and beef. Return the beef to the pot. Add the beef bone broth, carrots, potatoes, thyme, rosemary, and bay leaves. Bring to a simmer.
Simmer. Cover and simmer gently for about 1 hour (longer the better), or until the beef is beginning to become tender.
Add the squash. Stir in the butternut squash and continue cooking for another 20–25 minutes, until the beef is tender and the vegetables are cooked through.
Thicken if needed. If you'd like a thicker broth, whisk the flour with a few tablespoons of cold water to make a smooth slurry. Stir it into the simmering stew and cook for 2–3 minutes until thickened.
Finish and serve. Remove the bay leaves. Taste and adjust the salt and pepper. For an extra rich finish, stir in a tablespoon of butter just before serving. Serve warm with crusty sourdough bread or cornbread.