Depends if you play on mobile or pc. Pc, no need to overwrite anything, you can completely delete previous game folder.
If mobile yes I think overwrite is needed, but I can barely test android myself so I have almost 0 knowledge, if another androider can join in to explain would be great ^^
Nope!
Saves transfer. They are located in game folder, but they are also saved in appdata folder, which isnt affected at all by you deleting the normal game folder.
You only need to start over with a New game if you used Walkthrough mod previously as it's no longer supported. Or if I make an announcement that starting over is required ^^