You will be having 2 locations for your saved files
1- the location of the same game and
2- on your C:\Users\%username%\Appdata\Roaming\RenPy
the answer is, even if you deleted the old game, with the new updated game extracted to any location, go to load a game and you can load your previously saved files.
or, you may copy the old save into your new game..
Correction;
reference to your question,
i have been told that for a reason, people who downloaded the new version of the game, cant access the old saves.. and/or to overwrite a save...
for me it is always a pleasure to re-do everything from the start, because sometimes Hyao changes/edit/update things from the early stages.. and i want to check them all