Combine the flour, brown sugar, chile powder, garlic, thyme, 2 teaspoons salt and a few grinds of pepper in a small bowl. Sprinkle all over the short ribs and rub into the meat. Arrange the ribs in a single layer in a 6-quart slow cooker. Sprinkle any of the remaining flour mixture on top.
Whisk the apple butter, mustard, ketchup and cider in a medium microwave-safe bowl. Microwave until very hot, then transfer to the slow cooker. Cover and cook on high, 4 hours.
Using tongs, turn the ribs in the sauce to coat, then remove to a bowl. Skim off the fat from the sauce (there will be quite a bit), then return the ribs to the sauce and add the carrots and scallions. Cover and cook on high, 2 more hours. Serve with cornbread.