Preheat the oven to 250 degrees. Heat the oil in a large dutch oven or pot oven-safe up to 250 degrees over medium heat. Add the bacon and cook until crispy on both sides. Remove the bacon and set it aside.

Pat the beef cubes dry with paper towels and sprinkle them with salt and pepper. Cook them in batches until browned on each side, making sure they're in one even layer on the bottom of the pot, about 5 minutes. Remove them and set them aside.

Add the onions, shallots, and garlic to the pan and sauté until translucent, about 10 minutes, stirring every few minutes. Add the carrots and parsnips and cook for an additional 5 minutes. Add the cognac and step back, use a match to ignite it to burn off the alcohol. When the fire dies out, cut up the crispy bacon into smaller pieces and add it and the beef back to the pot.

Add the wine and enough beef broth to just cover all the meat and vegetables. Stir in the tomato paste and thyme and bring the mixture to a simmer.

Cover, remove from the stove top, and place in the oven to continue cooking for 1 hour 15 minutes to 1 hour 30 minutes, or until the beef is tender and the vegetables are cooked through. Remove from the oven and place back on the stovetop over medium low heat.

Whisk together 2 tablespoons of melted butter with the flour until a thick paste forms. Stir this paste into the stew until it disintegrates, then add the frozen pearl onions.

In a several medium pot, sauté the mushrooms in the remaining 2 tablespoons of butter over medium high heat until they darken and become slightly wrinkled, about 6-10 minutes. Add the mushrooms to the stew and lower the heat to a simmer.

Allow to cook for another 20 minutes before removing from heat. Add salt and pepper to taste, garnish with fresh thyme, and serve immediately.