Preheat the oven to 250℉. Make sure to position the racks so that you can fit a large Dutch oven inside with its lid on.
With paper towels, pat the beef dry. Season with 2 teaspoons salt and 1 teaspoon black pepper.
Heat a large Dutch oven over medium heat. Add the bacon and cook, stirring occasionally, until the bacon is browned and beginning to turn crisp and the fat has rendered, about 10 minutes. With a slotted spoon, remove the bacon to a large plate.
Add the mushrooms and 1 tablespoon butter to the pot. Stir to combine. Sauté over medium low until the mushrooms are nicely browned and have given up their liquid, about 8 minutes. Add 1/4 teaspoon salt and stir coat. Let cook 30 additional seconds. Transfer to a separate plate or bowl that is separate from the bacon.
Increase the Dutch oven to medium-high heat. Add a single layer of beef cubes (be careful the cubes do not touch—you’ll need to work in batches) and sear until the beef is nicely browned on all sides, about 3 to 5 minutes (you do not need to cook it all the way through). Remove to the plate with the bacon. Repeat with remaining beef (take your time here and don’t overcrowd the pan. It’s worth it!).
Carefully pour in about 1/4 of the bottle of wine. With a wooden spoon, stir to scrape up any browned bits from the bottom of the pot (the dark stuff on the bottom is flavor!).
Reduce the heat to medium. Add the carrots, onion slices, and the remaining 2 teaspoons salt and 1 teaspoon pepper. Saute the onions and carrots until the onions are lightly browned, about 10 minutes, stirring occasionally.
Stir in the garlic and tomato paste and cook for 30 seconds, until very fragrant.
Return the beef and bacon to the pot, along with any juices that have collected on the plate. Add the remaining wine and broth.
Add the thyme. Increase the heat to bring the liquid to a simmer. Cover, then carefully transfer the pot to the oven. Bake the boeuf bourguignon for 1 hour and 15 minutes. The meat and vegetables should feel fork-tender.
Place the pot back on the stove. In a small bowl, mash the butter and flour together with a fork. Stir it into the stew.
Stir in the pearl onions and reserved mushrooms. Bring the stew to a boil, then lower the heat and let simmer for 15 minutes. Remove the herb bundle. Taste and adjust salt and pepper as desired. Sprinkle with fresh parsley. Serve hot with toasted baguette slices for soaking up the broth.
TO STORE: Refrigerate leftovers in an airtight storage container for up to 3 days.
TO REHEAT: Rewarm beef Bourguignon in a Dutch oven on the stovetop over medium-low heat or in the microwave.
TO FREEZE: Freeze leftovers in an airtight, freezer-safe storage container for up to 3 months. Let thaw overnight in the refrigerator before reheating.
TO MAKE AHEAD: Up to 1 day in advance, cut the beef, bacon, carrots, onion, and garlic as directed. Store each separately in the refrigerator.