Putting it in a USB enclosure won't help anything if the problem is NTFS. The drive would still use the NTFS file system.

I suspect your problem with the files is related.

I'm worried that, if Knoppix really can see a single file on the drive, there may only one file there! You might have to reinstall Windows entirely if there really is only one file there.
You could try opening a Konsole and running 'df'. See if there's a filesystem in the list with the name /dev/hda1 and see if the size in 1k blocks is about the size of your hard drive. If there isn't, your hard drive didn't mount correctly and Knoppix isn't reading the drive properly, which means your Windows installation could still be there.
(This is my system which has Linux installed on the hard drive. The printout on yours will look fairly different.)
Code:
bash-2.05b$ df
Filesystem           1K-blocks      Used Available Use% Mounted on
/dev/hda3             14000208   9802636   4197572  71% /
none                    257476         0    257476   0% /dev/shm
/dev/hda2             44031424  38393120   5638304  88% /win
Notice that /dev/hda2 is about 44,000,000 1k blocks. That's about 44 GB, which is roughly how large my windows partition is (42 GB). In your case, your partition will probably be /dev/hda1 and about the entire size of your hard drive.

The most I can suggest is going to the K menu->Penguin (knoppix) and selecting the Captive-NTFS option.
Captive-NTFS is a program that allows Linux to use Windows' NTFS reading utilities. It's not a perfect solution, but it ought to work. And don't worry if it can't find the files it requires on your hard drive, I recall that it also tries downloading the files from Microsoft.

Once that's done, yes you should be able to OVERWRITE the damaged file(s), provided you have a second CD drive or can put it/them on a floppy or find it/them online somewhere. That may not fix it, but that sounds as good as anything I can think of.

Once your PC is back up and running, I'd recommend installing Knoppix, rather than using Red Hat 6.1. Red Hat 6.1 is very old, and would be a pain to bring up to date even assuming it were possible. The most recent desktop versions from Red Hat apparently have bugs. Stick with Knoppix.