Keeping her locked in a pit for several weeks. She'd be starved, only given enough water to stave off dehydration (which Pinkie dumped on the filthy floor for her to lap up) and she'd be forced to sit near her own waste due to the small space in the hole. Apple Bloom would also leave plates of hot food right outside the cage, just out of reach. her wings would be left intact since the gate would keep her in. Eventually, once Fluttershy was completely broken, Apple Bloom would feed her, by tossing a wounded, bleeding Angel to see if Fluttershy would give in to her hunger.