Adjust oven rack to middle position and heat oven to 375°F Pat pork loin dry with paper towels and season with salt and pepper.
Heat 1 tablespoon oil in large skillet over medium high heat until just smoking. Place pork loin, fat side down, in skillet and cook, turning it several times until browned on all sides. 8 to 10 minutes. Transfer pork, fat side down to 13 x 9-inch baking dish and roast until thermometer inserted registers 85 degrees. About 25 minutes.
While pork roasts, cook remaining tablespoon oil and shallots in empty skillet over medium heat until golden brown, 3 to 5 minutes. Increase heat to high, add cider, apple butter, bay leaf and thyme and bring to boil. Cook until thickened, about 8 minutes.
After pork has roasted for 25 minutes, pour glaze over pork and roll pork to coat with glaze. Cook until internal temperature registers 145 degrees. 20 to 30 minutes more, turning over halfway through to recoat with glaze. Transfer pork to cutting board, tent with foil and let rest 20 minutes. Transfer glaze to small saucepan and whisk in vinegar.
Before slicing pork, pour accumulated juices from roast into glaze and warm glaze over low heat. Cut roast into 1/4-inch slices, transfer to platter and spoon 1/2 cup glaze over top.