Same process as always - download new folder, move saves over, then delete old game folder. Simply, if you don't delete your saves, they won't be deleted.
If you're updating via the patch process, the folder isn't deleted at all so you don't even have to worry about that small step.
Oh, and please don't slam the new game folder into the old one, that causes horrendous errors. Just follow the actual update process, it's not difficult.