In my opinion you should concider partitioning your hard drive. This way you have your operating system on C: drive and store all your important files on a different partition that way if you ever need to reinstall or format the windows partition you will not loose any of your valuable data.
Doing as reinstall of windows should replace the missing file without loss of any data. As Mercenary Pilot says there is a repair console included in the windows CD that you can use to repair the damaged file.
Good Luck Allen