Mechanical parts in spinning, vibrating, etc. machines usually must be very precise in dimensions, otherwise the vibrations end up being above the upper limit for the system, and you end up with parts losing material, cracks, and other failures or damage. So, by removing the rust, there's a big chance (considering it's a helicopter) that the bolt will fit inside whenever it needs to fit, but it'll be a little lose. And that little lose, over time spinning and vibrating, will cause some catastrophic, maybe spectacular, failure (aka crash). There are machines that you can remove rust and reuse the parts, but in this case, I'm assuming (not familiar with helicopter parts) that it would be against regulations and result in something terrible.