No, saves are stored in two locations on PC, so you can delete the old version and DL the new one without doing anything else.
Eternum is hard to beat. Once in a lifetime is by Caribdis as well though, and despite it being his first game it has the same quality writing and humor. It's a bit short, but definitely worth playing.
Yeah you can no worries. Saves are also stored in the appdata folder under renpy.
