I just compressed my C: partition, which is the System and Boot partition, and could still boot fine. I did not think Microsoft would allow you to compress files necessary for your system to boot.
suggested earlier, the bootrec /fixboot
command is recommend for your exact situation. Although it assumes something corrupted your System partition, like a driver, or virus.
So, however you compressed the drive, might have led to a deeper problem than just a couple of files being bad.
But I was unable to duplicate your situation.....