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Chances are if other files got majorly damaged, whatever custom app you have may not run correctly. Note after any XP In place upgrade / repair installm you almost always have to boot into Safe Mode with Command Prompt first, install IE8, then reboot to normal, then clear update cache and run Windows Updates. What ended up working in a half assed way once for me, when even restoring the registry manually didn't help it be recognized, if making a full backup of the drive first, then doing a full install OVER TOP of the original Install (Without formatting), then manually restoring a backup of the registry from the backup drive I made.
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(Making backups of the ones you have first). Sometimes, SFC SCANNOW not working in Windows, but DISM still works properly and can fix the problems SFC can't. SFC SCANNOW Fails Fixed with DISM command. If it doesn't give you the option for a repair install when you boot the XP Disk and select install (Not recovery console), then chances are the registry is shot, or it's unable to mount the system hive of the registry.Verify you have the correct disc (Either XP Pro OEM, or XP Pro Corp/VLK in your case I bet), then try going into the System Volume Information folder and restoring a backup copy of all registry files from System Restore manually. In the beginning, you need to ensure that you run SFC SCANNOW command as administrator.
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