But if you don't transfer your saves manually, you will lose the main copy and only have access to the backup folders in the appdata folder (unless you keep all old versions).The issue is that you're attempting to transfer saves on a renpy game manually. You don't need to do anything but download the update and launch it. Your saves will be there.
I always move my saves, screenshots, and every other thing I have for every game to their new folder, because I don't want to lose anything. I have lost my saves because I forgot to copy them over before, and never want that to happen again.
No offense, but having to start over really sucks, even games I love. I don't even have time to replay short games I like, never mind ones I am more than two years into. Hell, I had to drop most of the games I play as it is. There are only a handful of games that I still drop almost everything to play each update.