Greetings, welcome to the forums.
I would not recommend the updater, because it takes much longer to download all files from the one and only updater server (or are there again a few?) than to download the whole new installer via BitTorrent (or possibly one of the HTTP mirrors).
It may be advisable to remove the previous version 0.4 for compatibility. Your game account will be kept, but you would possibly lose some customizations. But you can try just to overwrite the old version if you are not afraid of possible compatibility issues - I would just recommend to call the PlaneShift launcher once, set up all options, and close it: That should enforce updating the config files to a current state.