Deleting an OS command is not a good idea. Do you mean that it runs a chkdsk every time you boot your system? Or do you get a message about it / does it run when you try to defrag?
More detail about when the unexpected happens, what commands (if any) you have issued, and the messages that you see would be quite useful.
PS - If I had to take a flaming guess, you have a problem with the drive or its filesystem. But we really need more info.