Mix the flour and paprika together in a plastic bag. Season the beef with the sea salt and black pepper and transfer them to the plastic bag. Toss everything together to coat.
Heat up 2 tablespoons of the olive oil in a cast iron dutch oven over medium flame. Add the garlic cloves and sear until golden on both sides. Transfer to a bowl. Shake any excess flour from the beef and sear each cube for a couple of minutes until golden brown at the edges. Work in batches so you don’t overcrowd the pot and add 1 tablespoon of olive oil in between batches if necessary.
Transfer them all to the bowl with the garlic and cover with plastic wrap to keep warm.
Add one more tablespoon of olive oil to the pot and saute the onion with a pinch of sea salt until translucent. Add the red pepper flakes and cook one more minute.
Meanwhile save two strips of orange peel from the blood oranges and zest the rest and reserve. Squeeze 1 cup of juice from the oranges and add it to the pot together with the balsamic vinegar. Using a silicone spatula make sure to scrape all the brown bits from the bottom. Add the bay leaf, cloves, thyme sprigs and orange peels and allow to simmer for 3 minutes.
Add the beef cubes with all the juices and the garlic back to the pot and stir to combine. Add the water and bring to a simmer. Cover with a tight lid and transfer to a 350 F degrees oven. Let it cook for 2 hours.
Add the butternut squash and carrots to the pot, give it a good stir, cover tightly with the lid and let cook in the oven for an additional 45 minutes or until the meat and vegetables are tender.
Discard the bay leaf and thyme sprigs and gently stir in 1/2 teaspoon of the reserved orange zest.
Serve hot sprinkled with the parsley, orange slices, red chile and a pinch of freshly grated nutmeg.