Re: "For example I have nodes with IDs n0, n1, n2, n4, n7 and I want them to be n0, n1, n2, n3, n4."
I know what "resetting/reassigning/reordering" means. What I do not know is what/which node ID you mean. There is no such thing as a node ID in yEd. So what is it you are asking about?