1. Saves are kept separately from game as far as renpy is concerned.
2. Using saves from old versions in renpy games is not advised. Skipping through everything you've seen on a fresh save is the best way to avoid bugs and errors.
Oh. When I play the new updates, I just make pick up from a save file I made at the end of the previous update and continue where I left off. I haven’t encountered any bugs or errors, but maybe that’s just dumb luck