Score a shallow X on the root end of each pearl onion. Drop into boiling water for 60 seconds, then transfer to a bowl of ice water. The skins will slip off cleanly. Pat the peeled onions completely dry — surface moisture prevents caramelization.
Pat the beef cubes completely dry with paper towels. Season generously on all sides with salt and pepper. Heat 3 tablespoons olive oil in a large Dutch oven over high heat until it just begins to smoke. Sear the beef in batches — no more than a single layer at a time — for 3–4 minutes per side until deeply browned. Transfer to a plate and set aside.
Wipe out any burnt bits from the pot. Over medium heat, melt the butter with 1 tablespoon olive oil. Add the pearl onions and the sugar. Cook, turning occasionally, for 8–10 minutes until golden brown on the outside. They should be colored but still firm. Remove and set aside.
Cook diced onion in the pot over medium heat for 5 minutes until softened and lightly golden. Add garlic and tomato paste; cook another 2 minutes until fragrant.
Pour in the red wine and use a wooden spoon to scrape up all the caramelized bits stuck to the bottom of the pot. Let the wine bubble and reduce by half, about 3 minutes.
Add crushed tomatoes, beef stock, red wine vinegar, cinnamon stick, whole cloves, allspice berries, and bay leaves. Return the seared beef to the pot. Bring to a gentle simmer.
Cover and braise at 160°C (325°F) for 1 hour 30 minutes without disturbing.
Gently nestle the caramelized pearl onions into the pot. Do not stir — ease them in and return to the oven. Braise another 45–60 minutes until the beef yields easily to a fork and the sauce has thickened.
Remove whole spices. Rest at least 15 minutes before serving. Best made a day ahead: refrigerate overnight, skim fat from the surface, and reheat gently.