I personally believe that the Black/Golden City is Arlathan. To mention something that has not been brought up in this thread yet, the codex entry Arlathan: Part One contains the following:
"In those ages, our people called all the land Elvhenan [...] And at the center of the world stood the great city of Arlathan [...]"
So, as history remembers it, Arlathan stood in the centre of the world. Meanwhile, the Black/Golden City is located in the centre of the Fade. Maybe that is what history remembers.
Regarding the Fade before Veil, I don't think it was separated from the rest of the world like some here argue. It was a part of it. It wasn't, perhaps, easily accessible, but under the right circumstances one could experience it.
I see it a bit like experiencing sight. You have to open your eyes to see things, but that doesn't mean that what you see is not part of the world. I think the Fade worked similarily in that you had to achieve a certain state of mind to experience the fade, but it was always there, even if you didn't directly experience it.
Relating this to the shattered library, it was built by intertwining the physical world and the Fade. It's like a house that's built of wood and stone, except in this case the wood is physical and the stone is made from the Fade. When the Veil was put up it's not so much that it lost its connection to the fade as it is the wood and the stone couldn't interact the way they had. This lead to the whole structure crumbling, because the physical parts were dependent on the Fade part and vice versa.
If it had been built entirely from Fade stuff, maybe it wouldn't have broken, and maybe that's what Arlathan was, and thus how it survived to become the Black/Golden City.