Open Question: Does reinstalling windows wipe the whole hard disk?
I think the best thing to do is do a clean install of the operating system. Reinstall all your software AGAIN! (yeah, I know you hate it)...and this time, BACK IT UP with backup software to an external USB backup hard disk. That way, you have an uncorrupted clean install copy (equivalent to a factory install) which you can revert to in case of corruption. What I would do is to burn this clean install of everything to a small hard disk and then take the hard disk out of the computer and store it in a clean, safe, protected place. That way, if you get corrupted again all you have to do is swap out hard disks. You could clone a copy of this to another hard disk which you will now use while having a back up copy in storage. What I am suggesting is not quite like a mirrored RAID configuration because a true mirrored RAID configuration writes a copy continuously to a mirrored hard disk. What I am talking about here is just having a clean install of the OS + all your software and then taking it out and storing it rather than having a continuously backed up mirrored RAID image.
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