NTFS problems are not insurmountable.
Check out the home pages on the NTFS drivers. Their problems tend to be with permissions/ownership of files and allocation of space if writing a new file. With few or hard choices with a Windows system, I would delete files with little anxiety; rewrite deloused files with little anxiety unless they expand radically, which I would view as unlikely, and I would be apprehensive about writing a new file. You can write a backup within KNOPPIX to a USB or firewire drive. If Windows ran afterwards, I would create a proper backup of all data, in case of a crash.
I would view the O/S as suspect, but then it is a Windows system and suspect to begin with. I have a blow it all away and reload about once a year on my machines. It usually involves one intensive session and then a week or so of intermittant tinkering to get everything reloaded and all of the data retrieved from backups i.e. to get everything arranged. I am more conservative with the machine my wife is on, because she doesn't respond well to needing a piece of software reloaded or some data file retrieved from a backup. I keep good backups of that box and pray a lot. It is an older box 1 Ghz with W2K. I have been unsuccessful in persuading her to move to a notebook.
