Preheat the oven to 325 degrees F. Heat the olive oil in a large Dutch oven over medium- high heat, then add the bacon and cook until crisp, about 10 minutes. Use a slotted spoon to remove the bacon to a large plate.
Meanwhile, dry the beef cubes with paper towels and season them with salt and pepper. In batches in single layers, sear the beef in the hot bacon drippings, turning to brown on all sides, 3 to 5 minutes per batch. Remove the seared cubes to the plate with the bacon and continue searing until all the beef is browned.
Add the thyme, carrots, onion and tomato paste to the pot. Toss in the fat in the pan and cook, stirring occasionally, until the onions are lightly browned, about 10 minutes. Put the beef and bacon back in the pot with their juices. Add the wine plus enough beef stock to almost cover the meat. Bring to a simmer, cover the pot with a tight-fitting lid and bake for 1 1/2 hours.
Put the butter and flour in a small saucepan over medium heat and whisk together constantly until the raw flavor of the flour cooks out, 2 to 3 minutes. Put the beef Bourguignon over medium heat, stir in the butter mixture and cook until the stew thickens and the meat is very tender when pierced with a fork, about 15 minutes. Remove the thyme stems and serve.