This is why my work documents and data are always on a second drive (or partition if hardware is limited). I haven't used the default Windows folders for years and it's only some software creating folders under "My Documents" that I just ignore. You never know when you'll have to reformat the main Windows drive. It also proved convenient when I changed computers as I just plugged in the data drive I had always been using, and all my familiar documents are there. Of course, there's also the cloud to backup the more important stuff.
That's why on linux you can mount your home directory to a separate partition. You can reinstall the OS but still keep all your files and settings intact. And even better, it's the default location like "My Documents" so the OS and apps know where to look for things.
