Anyone else here instinctively take measures to hedge against windows unreliability??
Yes, I install Linux.
More helpful advice, I separate my data from my machine (or at least I am working too). I should be able to reinstall my OS without altering or touching my data.
You know how you get it? by fucking around and finding out! I'd say give it a go!
Do a dry run of the de-dup to make sure you don't delete anything you care about.