back up your saves, delete the entire folder, then get the downloader version. You can not overwrite the old version with the DL version. It will crash.
After installing the downloader version, you can drop your save files into the saves folder and launch. Launcher will let you download the latest files and you are good to go.
There is a 2GB limit for Itch, the downloader is required for them to keep adding more content. I dont know if they can do .part files for Itch.