I believe there is a bug in the universe_update() function in the API.
It appears to create the ‘APIUniverse’ universe correctly if it does not exist, and it sometimes seems to update (at least the first rule) the universe. But it does not remove all the previous rules from a previous update.
Hi Tony. When verifying that the API script changed the APIUniverse, you need to open the Universe page for some other universe, close that, then open the Universe page for the APIUniverse universe. Then it will be refreshed and have the changes you expect. You could also log off the site and log back in.