Pony problems?

Until recently, our stud was out with all the geldings. He proved that he can no longer have friends by cornering the pony and beating him up pretty good (until that, pony had been herd boss, that's why he was targeted). Pony has been vet-checked and had no injuries. However, I'm thinking his pony pride was hurt. He's become very shy and spooky. The stud has been locked up since this incident, but pony still doesn't want to come out of his stall. He'll start shaking when I go to halter him and pacing at the back of the pen. Any suggestions on helping him to regain his confidence? I love my spunky pony and want his attitude back. Thanks in advance.