Hi.
What I do is firstly I have a 3 tiered naming convention for the folders that store the renpy VNs (all VNs actually).
0 - [Devname] Game name [version] Date of last update
1 - [Devname] Game name [version] Date of last update
F - [Devname] Game name [version] Date of last update
The 0 folder is for the VN I am playing currently
The 1 folder is for a VN that I have downloaded but not started yet
The F folder is for a VN that I have finished and am waiting for an update.
The F folder simply contains browser bookmarks for where I can check to see if the VN has been updated, and it contains the "saves" folder from the "game" folder of the completed VN. This folder holds your save games.
So when I finish a 0 folder game, I cut the "saves" folder from the "game" folder and paste it into its 0 folder.
I then delete all of the game files (ie everything except the bookmarks and any saved screen shots).
Then I rename the 0 folder to an F folder, and wait for the next update.
This has never failed for me, unless the dev releases an update to the VN that changes the structure and won't handle old save games, then I have no choice but to start the game from the start.
I hope you find this useful.