unfortunately this wasn't the case for me - my saves didn't carry over and I had to start over again from the latest free version. I would suggest you keep a back up just in-case.
Emmm, that's weird. I've been playing the game since 0.7.1, and my saves always carry over (Oo). Maybe it's because I did not change the install folder? I only update the game by the itch app. But thank you for your suggestion, I just backup my saves ( just in case, some saves are at the beginning of some sweet events of Rae.）