If you're on Android you shouldn't be deleting anyway - just download the update and install on top of the old update. If you're on Windows, Linux or Mac you can delete the game and the saves will still be there.
If you don't want to download the entire update each time, the Itch launcher allows you to download patch files, which are much smaller (around 25MB each). But be aware that the launcher will sometimes delete manual saves! (Autosaves are safe, though).