Does running System File Checker overwrite Windows Updates?

I had a problem on my Windows 2000 PC that I thought may have been due to corrupt system files so I ran the SFC which replaced a few files. However, now I don't know if all the security and other updates that I installed using Windows Update prior to running SFC are still installed on my PC. When I run Windows Update now, it says there are no pending updates but I don't know if this is correct or not. Can anyone advise me on this?