I ran into a major glitch/bug after the update: I'm only launching into the Progeny Simulator. I'm finding this more anoying than having my saves deleted after each update.
make sure you're not overwriting folders when you download a new version.
Just extract the new version somewhere and move ONLY the savefiles you want to transfer in there.
I reinstalled the game and it works, this was long before I read your reply.
As for my saved files, I'm gonna need a step by step guide. So far I've only been updating from itch.