I think Arlathan and the Golden/Black City are one and the same and, Skyhold was once the anchor point between it and the rest of Elvehan. The Veil was the defense that kept darkness out of all of Arlathan but, when the magisters managed to breach it, the elves unleashed powerful, dark magic to destroy them and, instead created darkspawn. Only Skyhold remained protected by the magic that kept darkness away. Likely the elves there quickly separates Skyhold form Arlathan to preserve what they could.
Knowing what had happened the would have also reenforced the wards that protect Skyhold, making it impossible for anything corrupted to come near it. That's why Solas knew it would be a safe place for the Inquisition, those wards are still in place, perhaps because he's been keeping them that way. Solas may be the guardian of Skyhold.