Add mushrooms, onions, and carrots, scraping down the brown bits from the pan, stirring occasionally, for about 5 minutes. Sprinkle in flour, stir to mix and coat veggies. Add broth, wine, pepper, and thyme; return beef to the pan along with any accumulated juices. Bring to a boil, reduce heat to medium-low. Cook, uncovered, for 45 minutes, stirring occasionally.