In a 6-to-8-quart saucepan with a tight-fitting lid, cook bacon uncovered over medium-low heat until browned, 10 to 15 minutes. With a slotted spoon, transfer bacon to a paper-towel-lined plate; set aside. Reserve bacon fat.
Season beef generously with salt and pepper. In a large bowl, dredge beef in flour, shaking off excess. Raise heat to medium. Working in two batches, brown beef in bacon fat on all sides, without crowding, about 10 minutes per batch. Transfer each batch to a bowl.
Pour 1/2 cup water into pan; bring to a boil. Cook, stirring, to loosen browned bits, until liquid has reduced to a few tablespoons, 2 to 3 minutes.
Add onion and garlic; cook, stirring, until slightly softened, 3 minutes. Add tomato paste; cook 1 minute.
Add carrots, meat (with juices), wine, thyme, and reserved bacon. Bring to a boil. Reduce heat, cover, and simmer over low, stirring occasionally, until meat is tender, but not falling apart, 3 to 3 1/2 hours.
Skim fat off surface of stew; discard. Stir Roasted Mushrooms and Pearl Onions into beef; season with salt and pepper. Serve, or refrigerate, covered, up to overnight.