Take short ribs out of the refrigerator and out of the package. Let them rest and warm up on the cutting board, on the counter, for about 30 minutes before cooking.
Slice shallots and set the aside. Peel, smash, and mince garlic and set it aside as well. Measure remaining ingredients for the sauce and set aside.
Pat the beef dry with a paper towel and season generously with salt and pepper on all sides.
Sear short ribs:
Preheat a large pan over medium-high heat and add oil. Sear the meat in batches so they are not overcrowded. Sear them on all 4 sides until golden brown.
Take the meat out and set it in a large 9x13 casserole baking dish.
Preheat the oven to 325°.
Red wine sauce:
Using the same pan where you seared the meat, add a little more oil if needed and add sliced shallots. Sauté until softened and starts to brown.
Add minced garlic, stir, and sauté until fragrant.
Sprinkle flour over onions and garlic and mix until they're coated.
Pour in the wine slowly while slowly stirring and scraping the bottom of the pot. Stir in apple cider vinegar, beef stock, tomato paste, and seasoning.
Mix in seasonings and let it come to simmer. Simmer for a few minutes until sauce starts to thicken.
Pour the sauce over the beef in the casserole dish and make sure it's nestled well.
Cover the dish with the aluminum foil and cook in the oven for 1 1/2 hours.
Take the aluminum foil off and flip the short ribs. Cook for another hour.
Take the dish out of the oven and let it rest about 15 minutes before serving.