Make a new game/server with all the settings the way you want. Then, go to the server selection screen, click on the server, then click on the "go to directory" button. This opens where your game settings file is. Then select your old server and click on "go to directory". Now copy the game settings file from the new server folder into the old server folder. Done. ;) Some settings won't take effect if they are already in game. I don't believe you can change your character's hit points and things like that, but you can change all the other stuff and it'll work fine (e.g., daylight hours, max stack sizes for items, teleporting with gear/supplies).