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Preheat the oven to 325ºF.
Pat the beef dry with a paper towel. Season the roast all over with 1 tablespoon salt and 1 1/2 teaspoons pepper. Dredge the whole roast in flour, including the ends. In a large Dutch oven, heat 2 tablespoons olive oil over medium heat. Add the roast and sear for 4 to 5 minutes, until nicely browned. Turn and sear the other side and then turn and sear the ends. This should take 4 to 5 minutes for each side. Remove the roast to a large plate.
Add 2 tablespoons olive oil to the Dutch oven. Add the carrots, onions, celery, leeks, garlic, 1 tablespoon salt, and 1 1/2 teaspoons pepper and cook over medium heat for 10 to 15 minutes, stirring occasionally, until tender but not browned. Add the wine and Cognac and bring to a boil. Add the tomatoes, chicken stock, bouillon cube, 2 teaspoons salt, and 1 teaspoon pepper. Tie the thyme and rosemary together with kitchen string and add to the pot. Put the roast back into the pot, bring to a boil, and cover. Place in the oven for 2 1/2 hours, until the meat is fork tender or about 160ºF internally. Turn the heat down to 250ºF after about an hour to keep the sauce at a simmer.
Remove the roast to a cutting board. Remove the herb bundle and discard. Skim off as much fat as possible from the sauce. Transfer half the sauce and vegetables to a blender or a food processor fitted with the steel blade and purée until smooth. Pour the puree back into the pot, place on the stovetop over low heat, and return the sauce to a simmer. Place 2 tablespoons flour and the butter in a small bowl and mash them together with a fork. Stir into the sauce and simmer for 2 minutes, stirring until thickened. Taste for seasonings. Remove the strings from the roast, and slice the meat. Serve warm with the sauce spooned over it.