Well the problem should come from the use of duplicate finder.
If you did a run including all files with the wildcard *.*, so you got a lot of system files in the result, which are absolutly not to remove as the handbook tells you on page 43.
If you did a backup with jv16 PowerTools you could restore the mistake, using the Backup tool you find in File menu. But if you have not I think the onliest thing will be a repair run by your Windows CD.
May be somebody else could give you a better tip?
Jean-Paul