Guys! i have a problem. need help! Afraid of losing all csgo settings.

So i just bought new parts for my computer, cause i needed better cooling and other stuff, and now i cant start windows, and suspect that i need to reinstall windows. But the real problem here is the save files for csgo, what will happen to the configs and stuff. if i have windows on a ssd, and steam files on a hdd, will the csgo files be deleted when i reinstall?