It shouldn't matter whenever you replace all the game files, or just extract it to a different folder.
It would matter if scav had its save files inside its game folder (I haven't played in quite some time, but I don't think scav saves anything, right?). Then you would need to move the save folder if you extracted the updated ver somewhere else.
Though, as someone pointed out, itch has a client you can get with updates! (first time I hear about it lol)