I don't think any of the special ability guys can repair a totally broken shaft. Sounds like it's 100% destroyed, which means you get the shaft.

Sucks, but same with rudder, you lose it, you can't turn and you're done in.
Are you playing stock? The damage zones in stock are poor and you see more damage like this. Supermods correct it to a degree. I can't recall the last time I lost a shaft or rudder.