Your case might be more complex than I imagine, but let's assume it's simple.
If you have the system running and an external drive (or a usb drive, or just google "drive" cloud) save your stuff to it. If not sure, then just dump everything to it.
Make sure the stuff is stored and accessible on whatever storage you used. You can never be safe enough. Make sure the backup has all the things.
Then just wipe drives and install mint again, with drives/partitions as you need them.
btw, having both windows and mint installed is not necessarily a bad thing, if you can boot both.