Depends on the platform, most of the time it's all done automatically.
On android, for your own good, never uninstall, just update the apk.
All other platforms is automatic since the engine keeps copies of the savegames in a folder separate from the game's files.
I seriously recommend using the itch.io launcher to keep the game up to date, makes things way easier, since you don't have to redownload the entire game every time.