What I do is install the new version and play on it before deleting the last one, all of my saved games port to the new version and then I can delete the old one. Only did it once tho so it might not work every time.
No, you can delete the game completely, and the saves will still be there. This game saves stored at User\AppData\Roaming\RenPy as well as all the other renpy games.
