Combine remaining 2 1/2 cups beef stock, wine, and thyme, and bring to a boil. Cook until reduced to 1 cup (about 25 minutes). Discard thyme sprigs. Combine 1/4 cup stock mixture and flour in a small bowl, stirring with a whisk until smooth. Add flour mixture to stock mixture. Bring to a boil; cook 1 minute, stirring occasionally. Remove from heat, and stir in remaining 1/4 teaspoon salt, remaining 1/4 teaspoon pepper, butter, and truffle oil. Serve sauce with beef.