Unless the flow was hard enough to injure him, he is probably just annoyed. I assume that this was a brief time when the flow was directed near him. Certainly you should not keep a strong flow aimed at him. Make sure your powerhead intake is covered by sponge or something. Powerheads have probably killed as many anemonees as bad lighting.
I would leave him alone and keep an eye on him. If the conditions in the tank are good, he will be fine. He may decide to move back where he came from though, if the lighting and current are to his liking.