Preheat the oven to 325. Adjust the rack to the middle to make room for your dutch oven.
Sprinkle the short ribs evenly with salt and pepper. Add the flour to a plate and roll the ribs on all sides (even the ends) to coat. Set aside, and heat the oil in the dutch oven over medium high heat until just shimmering, about 3 or so minutes.
Add the ribs, a few at a time and sear until golden brown on all sides, turning every minute or two. Remove the ribs to a plate if needed and repeat with any ribs that wouldn't fit, then place all the ribs on a plate while the onions cook.
To the fat remaining in your pot, add the onions and saute until just softening--6 to 8 minutes. Add the ribs back in then add the cider, broth, wine if using, carrots, garlic, thyme, apple, and bay leaves.
Cover and bake until the ribs are fork tender and the meat is falling off the bone. That was about 3 hours for me. Check yours halfway through cooking to make sure the liquid isn't evaporating.
Once out of the oven, remove any excess fat from the sauce if needed. Use a ladle to gently scoop any fat from the surface or use a fat separator.
Serve the ribs warm over mashed potatoes with a bit of fresh thyme on top.