The latest version contains every part that has been released so far, so it's the only file you need to download. Your saves and gallery unlocks are kept on a different area of your computer than the game itself, so it's also safe to delete the old game version and then open the new game version to continue playing with your save data intact.
Since the game is in-development, there may be times where the game pops up an error after you load a save to continue from one game version to another. If that happens, the quickest way to resolve it is start a new game, then use the skip option to zoom back to where you left off. The game keeps track of any dialogue you've already seen, so you won't need to click to proceed through old content except to reselect choices.
Itch.io actually has an app you can use to download and update games, which may make the process easier than downloading it manually. There's info on that here: https://itch.io/app