Pat the short ribs dry and season generously with salt and pepper. Heat the beef tallow in a large Dutch oven over medium-high heat. Sear the short ribs for about 3–4 minutes per side until deeply browned. Remove and cover in tinfoil, store in refrigerator.
Reduce the heat to medium-low and add the butter and thinly sliced onions to the same pot. Cook slowly for 35–45 minutes, stirring occasionally, until the onions are deeply golden and caramelized. Leave the pot uncovered so the moisture can evaporate and the onions turn golden instead of steaming.
Add the minced garlic, thyme, and bay leaves. Cook for another minute until fragrant.
Pour in the red wine, scraping up all the browned bits from the bottom of the pot. Let simmer for 3–5 minutes, then stir in the apple cider vinegar.
Return the short ribs to the pot and pour in the beef and chicken broth. Add the bay leaves and bring everything to a gentle simmer.
Cover and cook on low for 3–3.5 hours, until the beef is incredibly tender and falling off the bone.
After simmering, remove the short ribs and skim off any excess fat from the surface of the broth with a spoon. Shred the beef, discard the bones, and return the meat to the pot.
Ladle the soup into bowls and top with toasted gluten-free sourdough and freshly grated Gruyère cheese! Broil the bread and cheese in the oven for a couple of minutes until melted.
