Divide the beef along the natural muscle seam into 7 to 8 large sections, cutting any oversized pieces to make them more or less even. Put the beef in a shallow glass of ceramic container that fits the meat snuggly. Season it generously with the kosher salt and pour in the wine, the 1/4 cup olive oil, and thyme. Cover and marinate the beef in the refrigerator for 3 to 12 hours, turning the beef once. Drain the meat and blot dry with paper towels, reserving the marinade.
Heat the remaining 2 tbsp oil in a Dutch oven over medium heat. Cook the onion and carrots, stirring occasionally, until they are speckled brown, about 7 minutes. Use a slotted spoon to transfer the vegetables to a bowl and set them aside. Increase the heat to medium high and brown the beef on all sides, about 10 minutes total. Sprinkle the flour over the meat and continue to cook, turning often, until well browned all over, about 6 minutes more. Don't rush this step; taking the time to let the meat develop a dark crust produces the richest sauce.
Preheat the oven to 275°F. Return the vegetables to the pot with the meat, marinade, and the brandy. Bring the liquids to a boil and scrape the bottom of the pot clean to release all the browned bits. Reduce the heat to low, and add the garlic, pepper, parsley stems, and bay leaf. Cover the pot and braise it in the oven until a fork readily pierces the meat all the way through, 2 to 2 1/2 hours.
Meanwhile, if using raw pearl onions, you will need to peel them first. Bring a small pot of water to a boil over medium-high heat. Plunge in the onions and boil for 2 minutes. Drain, cool, and trim the root end to pop them from their skins. Melt the butter in the medium skillet over medium-high heat and cook the onions until they are translucent and tender, about 3 minutes. Slide them out of the same pan and cook them, stirring occasionally, until they are well browned, about 8 minutes. Put them in the dish with the onions.
Use a slotted spoon to lift the meat and vegetables from the broth into the serving dish with the onions and mushrooms, parsley stems, and bay leaf. Skim any fat from the stock, strain it through a sieve into a saucepan, and simmer to reduce over low heat until it coats the back of a spoon, about 5 minutes. Taste for salt and pour the sauce over the beef and vegetables in the bowl, sprinkle with the chopped parsley, and serve.
Source: Curry, Lynne. "Beef Bourguignon." Pure Beef: An Essential Guide to Artisan Meat with Recipes for Every Cut. Pennsylvania: Running Press Book Publishers, 2012. 126-127. Print.