Estinien actually is a huge gaping plot hole in this patch if you've finished the DRG job questline. He's apparently back to part of the Ishgardian forces again and being an Azure Dragoon, and even references the conclusion of the final job quest... but then if you talk to Alberic then he says that Estinien is still missing and that the post of the Azure Dragoon is vacant. Not to mention the... repercussions if it got around that Estinien decided to give into the dragons.
Make up your mind SE! :P