In a non-reactive dish, combine chunks of beef, red wine, pearl onions, carrots, thyme, and bay leaf. Cover and refrigerate for 12 to 24 hours.

Pour the reserved marinade into a saucepan. Bring to a gentle boil and reduce by half for 10-15 minutes. Set aside to cool.

Remove beef from marinade and pat dry. Season with salt and pepper. In a heavy pot, heat oil and brown beef in batches for 3-4 minutes per side.

In the same pot, add diced bacon and cook until golden. Stir in mushrooms, then add pearl onions and carrots. Sauté for 5-7 minutes until tender.

Add butter and flour to the pot, stirring to create a roux, then add tomato paste and cook for another minute. Gradually whisk in the reduced wine and beef stock.

Return browned beef and bacon to the pot, add thyme and bay leaf, and bring to a simmer. Cover and transfer to a preheated oven at 325°F.

Cook for 1.5 to 2.5 hours. Stir in sautéed onions and mushrooms after an hour. Check for doneness after 2 hours.

Remove from oven, taste, and adjust seasoning with salt and pepper. Optionally, let rest overnight in the fridge.

Serve in bowls or over mashed potatoes with crusty bread.