I was struggling with this a little too. If you have a working client and GUI, all you need to do is stop the netclient service if it's running, which seems to stop anyway once the server is upgraded. Then download the new netclient .exe (not the MSI) and overwrite netclient.exe in program files (x86)/netclient. Start the netclient service and run the pull command. Might take a minute for the node to update in the WebUI