So with most of these kinda games the saves are also somewhere in your %appdata% area I think and it usually carries over no problem. I will say from experience some games may give you trouble backing up an old save if you reinstall windows. Idk why. IIRC this one was fine though.
Look for something called renpy or something I think? If you have the trouble I did with the other game anyway. To just download a new version of this game you shouldn't have to worry about saves at all though. Just unzip and launch the new version without doing anything else usually.
TLDR for what else I said, no you're fine. Just unzip and launch the new version and everything is there. The old version should be safe to delete if you're on a Windows computer, as the saves are elsewhere already. Other devices though, I don't know where the saves go.
