Sorry that your son just missed - a real pain!!
http://www.elevenplusexams.co.uk/11plus ... #section-B
You have to do exactly the same as an 11+ miss - so it's that same old answer, read the link above and try and get as much academic evidence as possible to prove that your son should be at a GS.
Obviously you will now be able to include academic evidence from his current school (tests/school reports etc) as well which will be vital in proving the 12+ did not represent his true academic prowess.