you mean the download files or the game data? the game data would be the save game, that does usually not change if you change installation data.
if you mean how to make the game be updated by that itch app, but not download it again, since you already downloaded it, no clue. but you can add installation directories.
you probably are following developers of your games, so, my first guess would be to just add the game to the app after an update, so you reduce unnecessary downloads.