You usually don’t have to worry about that since Ren’Py stores saves in two different places.
The places in question are as follows:
C:\Users\<<user>>\AppData\Roaming\RenPy\Testgame-1635123618<game install directory>\game\saves
The former is shared across all open instances of Goddesses’ Whim, and is potentially used by the Ren’Py Sync Server when moving saves from 2 entirely different devices.
TL;DR: You don’t need to worry about transferring saves (usually) when updating.