Preheat oven to 325 degrees. In a large Dutch oven, saute bacon over medium high heat until crisp. Using slotted spoon, transfer to paper towel lined plate.
Sprinkle beef with salt and pepper. Toss well in flour. Working in batches, brown in same pot over medium high heat until brown on all sides, about 8-10 minutes. Do not crowd pot. Transfer to large plate.
Add onions, carrots, 2 teaspoons kosher salt, and 2 teaspoons ground black pepper to same pot and cook until lightly browned, about 10 minutes. Add garlic and continue to cook for 1 minute more. Transfer to large plate with beef.
Add 1/2 cup broth and cognac to pot. Bring to a boil, scraping up any brown bits. Continue to boil until mixture is reduced to a glaze, about 5-6 minutes.
Return bacon, entire plate of meat, juices and vegetables to the pot. Add wine, remaining 2 1/2 cups broth, tomato paste, and thyme. Bring to a boil, stirring often. Cover pot and place in oven and cook until beef is tender and sauce has thickened, about 2 hours.
Add the mushrooms to the pot along with the pearl onions and butter. Continue to cook for an additional hour. Remove from oven. Let rest for 10 minutes before serving.
Serve with egg noodles, mashed potatoes or with crusty bread.