How can I upgrade a already scaffolded module?
First make sure you have committed everything or have a backup, then just scaffold out over the project again. yo will ask you for each file if you want to overwrite. For those files you haven't edited, just say yes. For the other ones, type d for diff and see what's changed. Then manually do the changes.
In the majority of cases you are only going to update the build scripts and the package.json file.