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To repair Windows OS system files you can use SFC Command and if you wish to replace windows installation you can boot from CD and go to setup then it will detect old installation then you can press "R" key, I'm not sure that what kinda files you trying to replace so try sfc first and if not go for the 2nd option
System File Checker gives an administrator the ability to
scan all protected files to verify their versions. If System File Checker
discovers that a protected file has been overwritten, it retrieves the correct
version of the file from the cache folder (%Systemroot%\System32\Dllcache) or
the Windows installation source files, and then replaces the incorrect file.
System File Checker also checks and repopulates the cache folder. You must be
logged on as an administrator or as a member of the Administrators group to run
System File Checker. If the cache folder becomes damaged or unusable, you can
use the
sfc /scannow, the
sfc /scanonce, or the
sfc /scanboot commands to repair its contents.
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System File Checker Tool Syntax
loadTOCNode(2, 'moreinformation');
Sfc [/Scannow] [/Scanonce] [/Scanboot] [/Revert] [/Purgecache] [/Cachesize=x]
•
/Scannow: Scans all protected system files immediately and replaces
incorrect versions with correct Microsoft versions. This command may require
access to the Windows installation source files.
•
/Scanonce: Scans all protected system files one time when you restart your
computer. This command may require access to the Windows installation source
files when you restart the computer. The
SfcScan DWORD value is set to
2 in the following registry key when you run this command:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Winlogon
•
/Scanboot: Scans all protected system files every time you start your
computer. This command may require access to the Windows installation source
files every time you start your computer. The
SfcScan DWORD value is set to
1 in the following registry key when you run this command:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Winlogon
•
/Revert: Returns scan to the default setting (do not scan protected files
when you start the computer).The default cache size is not reset when you run
this command. This command is equivalent to the
/Enable switch in Windows 2000.
•
/Purgecache: Purges the file cache and scans all protected system files
immediately. This command may require access to the Windows installation source
files.
•
/Cachesize=x: Sets the file cache size to x
megabytes (MB). The default size of the cache is 50 MB. This command requires
you to restart the computer, and then run the
/purgecache command to adjust the size of the on-disk cache. This command
sets the
SfcQuota DWORD value to x in the following
registry key:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\WinlogonFor additional information about the Windows File Protection
feature, click the article number below to view the article in the Microsoft
Knowledge Base:
222193 (http://support.microsoft.com/kb/222193/EN-US/) Description of the Windows 2000 Windows File Protection Feature