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Season short ribs with salt and pepper at least 1 hour (at room temperature) and as much as 48 hours (covered and refrigerated) in advance.
Heat oven to 300 degrees. Heat 1 tablespoon oil in a large Dutch oven over medium-high. Working in batches, sear short ribs until deeply golden brown on both large flat sides, 4 to 6 minutes per side. Transfer short ribs to a large plate or cutting board and drain all but about 2 tablespoons fat from the pot. Discard remaining fat. Repeat with remaining short ribs. Drain all fat from the pot and carefully wipe out. (No need to wash, just get rid of any scorched bits.)
In the same pot over medium-high, heat remaining 2 tablespoons oil, and add onions and garlic. Cook, stirring occasionally, until the onions and garlic get a bit of color, 4 to 5 minutes. Add honey and cook, stirring until it starts to bubble furiously, turning a darker amber brown and sticking to the bottom of the pot as it cooks.
Add vinegar and soy sauce, and, using a wooden spoon or spatula, scrape up the bits on the bottom of the pot. Bring to a strong simmer and cook to reduce by about half, 5 to 8 minutes. Add broth and thyme, and bring to a simmer. Season with salt and pepper and add short ribs back in, bone-side up, making sure they are as submerged in that braising liquid as possible. Cover the pot and place in the oven. Do not look at it or remove the lid for 3 hours. (Nothing bad will happen, promise.)
After 3 hours, check the short ribs, they should be extremely tender and nearly falling apart, almost having the jiggly texture of a baked custard or Jell-O. (If not, continue roasting another 20 to 30 minutes.) Remove from oven.
At this stage, you can remove the lid and using a spoon, carefully skim as much of the top layer of fat as possible. Increase oven temperature to 425 degrees, and return the pot to the oven, uncovered, to let the short ribs brown a bit on top and thicken the braising liquid a bit, another 35 to 45 minutes. (Alternatively, you can remove the short ribs from the oven, let them cool at room temperature and place in them in the fridge, overnight. When ready to serve, remove them from the fridge and using a spoon, scrape off the solidified fat on the top layer. Return the short ribs, covered, to a 325-degree oven until totally warmed through, 30 to 40 minutes. Remove the lid and increase temperature to 425 degrees, and continue to cook, uncovered, to let the short ribs brown a bit on top and reduce the braising liquid, another 35 to 45 minutes.)
Meanwhile, combine parsley and chives in a small bowl and season with flaky salt.
Remove the short ribs from the oven and serve straight from the pot or transfer them to a shallow bowl or plate with high sides, spooning the braising liquid over. Squeeze lemons over, letting the juice season the braising liquid. Sprinkle with parsley mixture before serving.