No, I never have. The game folder is on my desktop, and I just download the new update. Delete the old folder, and my saves are still in tact. I believe your game save data is saved in a separate location.
sorry I know someone else already told you how to do it manually, but if you want you can install the itch.io app and update the game. I do so since it's easier (I had no clue about what to do manually lol)
