You can update your @StarboundGame servers to the latest hotfix via the Mods section of your Control Panel at http://my.gameservers.com
I've just done this on my server and everything's working perfectly now. The process took around 20 minutes, though I had to redo my config file (to add server passwords / settings etc).
I'm not sure if we'll have to manually update the server like this for every hotfix, or if this "updatersync" mod will keep it updated automatically. We'll see soon I guess, as I'm sure Chucklefish will be releasing plenty of hotfixes.