This is a fairly easy thing to update. All you have to do is delete everything from the previous Fluid MC Stats installation (Except your Stats database of corse), Then upload the new files and follow the same install guide to make a new config.
This method is the most recommend because we have been adding many features that require the config to be changed. Instead of running the risk of trying to update the config and then ruining it, we would rather have the user just spend two minutes to make a new one.