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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.

It's easy. There's files named "save01, save02, save03... .rvdata2" in the game's folder, those are the save files. You can just move them into the new releases's folder.

Thanks.