Windows Repair Option Affects BootCamp?

I have a macbook with bootcamp, Windows and Mac OS X.
But one day, using the Windows partition, I switched their DLLS with the ones I downloaded from the internet coz some programme need them. So from then onwards, I restarted my macbook to get windows familiar with the new system files, but somehow, it began the loading loop problem. It never gets me to the desktop and it's stuck at the moving bar.
I can access Mac OS X until the desktop, but somehow in the log in page, it gave me the error the windows partition are not safely removed and it advises me to take it out, then use another windows pc to safely removed.. bla bla bla u know what it is, but I can access the windows partition fully from Mac OS X.
So now, the problem is that I want to get back my normal DLLs back so it can load to windows peacefully but i think the only way to restore the system files is to use the Windows XP CD (repair function)right? so if I were to boot from the CD, and use the repair windows finction, will it overwrite/upset bootcamp, rendering Mac OS X unavle to access since it's messing with the boot data?
Would like to seek advice from experienced users before I do anything... wouldnt want to make OS X dead like windows too...
Message was edited by: Reasoner

Start using backups and imaging or clone software. And don't make changes without figuring out how to get back or undo.
Upgrade to Windows Vista or 7.
You tried using Disk Utility Repair on the partition? And what if you boot XP CD or Safe Mode?

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