Upgrading to 6.5.5 will close the security issues associated with the older versions however, your config file will probably need to be redone.
The easiest way to rebuild a good config is to go through the install process up to the point where it says the next step is to create the tables. You just stop at that point, since the tables already exist, and you should be good.
You probably will want to check and see if they've done any more than that however. It's possible they've put in some backdoors as well.
