Skynet is still in development, so if new versions will be available on GitHub you will should update your clusters with newest version.
When you will download an update with new sources you will need to recompile your version of clusters.
After download new version just replace old /src/Skynet folder with new one and do not replace your code from /src/SkynetUser directory. At next, just recompile your clusters.
Your old config and listeners will be included into new version of Skynet's core.