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Keep your files in “My Documents” (and any other default media folders like movies and pictures; or on a separate drive) and you won’t lose shit other than installed programs when you re-install Windows.
Same goes for linux if you have /home on a separate partition/disk. That saved my ass more times than i am willing to admit…
Keeping home on a separate disk is the best way to go. A different partition is okay, but a different drive is even better.