that's sadly how the bureaucracy of different nations can mess you around. Sadly it will likely cost him all the fuss of going back and starting all over again. I wish you both luck.
I can only vouch for Australia but I was able to submit my plans on my current 5 month stay in conjunction to my return flight being 5 months after arriving and my 60 day visa was approved. If on your countries website it says a planned itinerary to explain the longer time period, you'll be able to do the same. Good luck