Preheat the oven to 350 degrees F.
Short Ribs: Pat the ribs dry and season generously with salt and freshly cracked black pepper, to taste.
In a large braising pot, preferably an enameled cast iron Dutch oven, heat the oil over high heat. Add the ribs in batches, so as not to crowd. Brown them deeply on each side and when all have been seared, remove them from the pot and add 1/3 of the beer to deglaze. Turn off the heat and scrape the fond from the bottom of the pan.
Sauce: Strain the fat from the Dutch oven, leaving the juices and return the pot to medium-high heat. Add the onions and cook until soft. Add the garlic and red pepper flakes, cook for 2 minutes more, then add both cans of the drained cherries. Bring to a simmer, add the chipotle paste and molasses and adjust seasonings, if needed. Reduce the mixture for 10 minutes at a simmer. At this point you can strain for a more elegant sauce, then add the butter, or just add the butter and leave rustic.
Put the beef ribs back in the pot, stir to combine with the onions and shallots, and pout in the remaining beer and sherry. Cover and roast, turning the ribs every 40 minutes. After 3 hours, drizzle in the molasses, return the lid and roast for 1 hour more.
Transfer the ribs and the sauce to a serving dish and serve.