How do you patch? Is it just the exe that needs to be replaced?
Originally I wanted to get that set up but there seems to be some weird technical difficulties with it. So you'll have to redownload the game and either extract the files to a new folder or replace every file, either will work.
Is the save file not in the same folder?
The save file is in AppData, so you don't have to worry about it when changing versions.
