huh, it doesn't delete anything just launch the new version.
Viewing post in ETERNUM [0.4] - PUBLIC RELEASE comments
No, you unpack the new version and just launch from the new version. In my case, I can find my save file when I launch from the 0.4 game.
However, if it doesn't work for you, you have to go to the save directory located in your 0.3 game. Just type save in the search bar in game folder and copy it and put it in the right directory in the 0.4 games. You can google "how to put saves in a renpy game".