Originally Posted by Brainiac
I'm not sure, but I seem to remember something along the lines of if it is the only pokemon you own that knows that HM move, It will not let you delete the move? someone should confirm this other then me, because for some reason this just sounds wrong.
That's correct. ^^ To make sure you don't lose your HMs for good, the game won't let you delete a HM move if that Pokemon is the only one that knows that move.
So teach Surf to another Pokemon in your game and you should then be able to delete it from Kyogre.