First thing is make sure that the disk is physically healthy ... I'd suggest running the short and long online self tests via smartctl (e.g. "smartctl -t short /dev/sda" -- the smartctl man page has more information). If SMART reports errors then probably the disk is on its way out and needs to be replaced. Note that fsck will generally refuse to run on a mounted filesystem (unless it's mounted read only). Why do you suspect the fsck was run while the root filesystem was mounted?
In principle you could use dd or similar to do a bitwise copy of the second server's hard drive onto the first server's disk (you'd have to have them both in the same machine and be very careful not to reverse the if and of arguments to dd). If these are production servers, though, why on earth don't you have back-ups already that you can just restore from?
It doesn't sound like you're particularly confident about the source of the problem, though, so for me step 1 would be getting a bit more certainty about that before trying to fix it.