1st, Generally with a few exceptions. You shouldnt remove files really, whilst your servers running it will most definatley cause you problems and the same goes for adding them. Consider it as you would an application install as thats what your doing here.
Editing the servertoolsconfig.xml is fine as the Author states. this can be done live. several mods allow this
Dont edit the main game .xmls at all with it running.
2nd you may still have that because you should also delete the servertools.bin from the games seed folder in your random gen saves I state this because you changed the mod to latest whilst the server is running so the servertools.bin and .dll wont have updated correctly at all nor will the mod
Especially If you still have the mod from using it in Alpha 15.
I know deletion will regenerate a new servertoolsconfig.xml file on reboot. They wont generate a new version of the .bin or .dll if they not been deleted. Especially when live as these files are already running
Please correct me if am wrong on this.
I hope this helps,
Ari