a precarious situation...what a horrid piece of software! Can you back up your files to CDR or another hd? I reinstall OSes pretty often so I keep my most precious stuff on at least two pieces of media in case something like this happens. Of course my advice would be to go for it as long as you have a means to get your system back the way you want it.
And for future reference, you've prolly figured this out already, but don't automate things in windows if you want security
Let us know what you decide