That depends a lot on the way the game saves data. For example, some games save on regedit, so it doesn't matter where you install the game the save file will be there. Some games save a file in a standard directory, so it doesn't matter where you install it too.  However, there are some games that save in a file in the game's directory instead, and installing in another folder would not have the save files (it might delete save data if you overwrite the old version too). I would reccomend extracting the update in another folder and test if it works. If not, try to find the save file from the old version of the game and drop it in the new one.