Begin by preheating your oven to 325 degrees Fahrenheit. Pat the short ribs dry with paper towels and season them generously on all sides with salt and pepper. In a large Dutch oven, heat the vegetable oil over medium-high heat. Sear the ribs in batches, making sure not to crowd the pan, until they are deeply browned on all sides. This step is crucial for developing a rich flavor base. Remove the ribs and set them aside on a plate.
Lower the heat to medium and add the diced onion, carrots, and celery to the same pot. Cook the vegetables for about 5 to 7 minutes until they begin to soften and the onions turn translucent. Stir in the minced garlic and cook for just another minute until it becomes fragrant, being careful not to let it burn.
Pour in the apple cider vinegar and a splash of the apple cider. Use a wooden spoon to scrape up all the browned bits, also known as the fond, from the bottom of the pot. These bits are packed with concentrated flavor that will season your entire sauce. Add the remaining apple cider and the beef broth, stirring to combine everything.
Nestle the seared short ribs back into the pot, ensuring they are partially submerged in the liquid. Add the fresh thyme, rosemary, and bay leaves. Bring the liquid to a gentle simmer on the stovetop, then cover the pot with a tight-fitting lid. Transfer the Dutch oven to the preheated oven and cook for about 3 hours, or until the meat is incredibly tender and easily pulls away from the bone.
Once the ribs are done, carefully remove them from the pot and set them on a serving platter. Skim any excess fat off the top of the cooking liquid. You can strain the vegetables or leave them in for a rustic feel. If you prefer a thicker sauce, simmer the liquid on the stovetop for about 10 minutes until it reduces and coats the back of a spoon. Pour the glossy sauce over the ribs and serve immediately.