I think she changed it because the scar caused Harry so much pain and a reminder of his parent's and everyone's death and of course Voldemort. I don't think Jo would have wanted that to be the last word because of this. Harry and everyone is happy and settled. 'All was well' is more concluding and reassuring after all those years and has a hundred different meanings in only three words. That's what I think, if only I could think like Jo, she is amazing! But I think it was a good choice to change the last words.