In a large pot or Dutch oven over medium heat, cook diced bacon until the fat renders and pieces are golden, about 8 minutes. Remove bacon with a slotted spoon and set aside.
Increase heat to medium-high. Working in batches to avoid crowding the pot, brown beef cubes on all sides (about 3 min per batch), seasoning with salt and pepper as you go. Transfer to a plate and set aside.
Reduce heat to medium. Add whole peeled shallots to the pot and sauté for 2 minutes. Return bacon pieces to the pot and simmer together for 10 minutes. Transfer shallots and bacon to a bowl and set aside.
In the same pot, sauté sliced shallots, sliced carrots, and minced garlic over medium-high heat for 3 minutes. Sprinkle 2 tablespoons of flour over the vegetables and stir constantly for 2 minutes to lightly brown the flour.
Pour beef broth into the pot while stirring to deglaze. Add tomato paste and Pinot Noir wine. Bring to a boil, then reduce heat to medium and simmer for 2 minutes. Season with salt, pepper, and thyme to taste.
Return browned beef, sautéed shallots with bacon, bay leaves, and a few parsley stalks to the pot. Stir gently to combine, then cover with a lid.
Place the pot on the lowest oven rack and braise at 180°C (356°F) for 1 hour 30 minutes until the beef is very tender. Taste and adjust seasoning if needed.
Finely chop the remaining fresh parsley and sprinkle over the top.