Yep, he is still in but with terminal, annual and resettlement leave could be finished work by October although his end point is Feb 2016. I will get him to get an official letter from his CO or Chief Clerk stating his end date but that he is on leave etc and hopefully that will suffice in lieu of discharge papers until they come through.
Having just spoken to someone at the embassy in Beirut I am feeling a bit less stressed. He indicated that if everything is in order and we have the necessary documents (we are just waiting on a new UK passport for him and marriage certificate extract) their processing time would be nowhere near that of the UK. Also, because we are UK nationals (although I am an Australian citizen by birth and hold both passports) and there is no biometric collection facility in Cyprus, he probably wouldn't need to do that either and we can do pretty much everything online. Not as bad as I first thought!