I have two characters because my first got messed up. But I wanna use it again when the patch comes out to fix it. Right now I've been doing this. I put all my saves for one character in a separate folder and keep on save list in the actual file. And if I wanna play the other character I just switch the files. This won't cause an issue for me when patches start coming out right?

No. It won't. It's no different than keeping past saves and reloading an old save.