Another option, if you are not sure or comfortable about loosing saves or not having some saves show "In Game" when you open save/load you can open the game folder in your old installation and the game folder in the new installation and copy your "saves" folder and paste it to the new game installation "game" folder so your game folder content looks the same. If it does not default to the same position automatically in the new folder (alphabetically by type) just right click in the open game folder panel back ground and scroll to "Refresh" and click. Folders should align in proper order then. To make sure your save folder copied over to the new game folder simply right click on the folder and select "Properties" at the bottom on both folders. Once they clock off the sizes they should match. Once matched. You are good to go for deleting the old game installation. I do it this way all the time. Saves on going into the user/name/appdata/roaming/renpy and searching for the backed up game saves to copy the saves from before the newer updated game version installation to paste them into the game so you can go back to check on a previous decision.
These steps also copy over your persist file so you don't have to reset your preferances settings in the new game update install.