If I get the patreon version do I keep my progress from the public.
Been thinking of upgrading, but I've invested a lot of time into this game. I'm concerned I'll have to start over, I'm too used to max creations points and I'm not looking forward to getting all the perk points again.

Well, the only thing different between those versions is that the paid features are unlocked. It won't be any different than updating your usual game.

And if you want to be sure, you can choose to go to save folder from Load screen and you'll find your profile + save files.