Preheat oven to 400°. Place beets, carrots, shallots and ½ cup oil in a roasting pan. Stir to coat vegetables evenly with oil. Add parsley and thyme, season with salt and pepper, and cook, stirring once, until vegetables begin to brown, about 20 minutes. Add lentils and 3 cups of water, stir, and then cover pan with foil. Cook until lentils are tender and all water is absorbed, about 1 hour.
Remove pan from oven. Remove and discard herb sprigs, then dress lentils with vinegar and remaining oil. Allow to cool slightly, then stir in chopped parsley. Adjust seasoning and serve.