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After upgrading Win2k hard disk, machine says ones of system files is missing/corrupt

I am in the process of upgrading the hard disk on my Win2k machine. I have made the partition active on my new drive and copied all the files via xcopy. But when I reboot the machine, it tells me that one of the system files is missing or corrupt. I tried fixing it using the emergency repair disk but to no avail. I have also tried directly copying the missing files from the old hard disk to the new one. Is there anyway to do this or will I have to use something like Partition Magic? Thanks.
The method you used sounds a bit dodgy. Instead of just copying the files from one disk to the other, I recommend that you use a disk imaging product such as Symantec Ghost, which is a wonderful inexpensive tool, to make a disk image, and then restore that image to the second disk.

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