When working with a server, just leave the instances connected when quitiing and saving in your DAW. After closing your daw you can close the server and discard the changes. When you reopen your projects, (with an empty server powered on) the projects will push data back in the server (will populate instances and plug-ins). If you forget to power on a server, just close daw project without saving, start the server, reopen daw project and you're all set.
You can also save both server project and daw project before quitting daw (and again leave all instances connected) just to be double sure you have your data saved.