We still dont know what he is really up to. But whatever that may be, I chose to serve him xD. And as soon as he asks me to give him the orb I am doing it no matter the consecuences. Therefore I am going to pour my blind faith on Nameless haha :P
But forgive me I havent answered your question. Without spoling too much I am just going to say that you will meet him again in a different place and the game will give you a new choice. In case you decide you side with Nameless you will witness a brilliant and clever use of the storytelling by Hyao itself. I reaaallly enjoyed this part. Many game developers should take notes.
And yeah, I dont want him to disappear either so lets just pray Hyao can give us a reasonable outcome in the end :)