in fresh install have all the files and in update only have the folders and files you've updated in. so if you're just updating 3.31 > 3.32 or 3.32 > 3.33 it will be better and easier.
The nature of Chevereto is a script that is highly customizable. That said, if you don't customize it (touching the script files) you can safely just re-upload everything, otherwise you need to do it manually.