The Quest where the Scions find out that the Isle of Val disappeared is "Build on the Stone". It's the last quest of 2.1 and in the quest right before it (The Gifted) we meet Elidibus for the first time and Minfilia asks the Students of Baldesion to look if they have any records on an Ascian in white. Even as far back as 2.0, the Sudents of Baldesion were researching on the nature of primals for the Scions and were regularly sending them reports.
In the scene where the Scions find out about Val's disappearance, they are quick to come to the conclusion that an Ascian had something to do with it since they can think of nothing else that could get through the island's wards. However, the Scions don't actually know what the other Sharlayan's saw at Val until much later. It's not until the end of 2.3 (Through the Maelstrom) that they find out that the Ilse of Val disappeared in a wave of aether so great it was thought to be similar to Ultima.
One of the very messy bits of the Eureka story is Emmerololth's apparent death. In 2.3 (What Little Gods Made Of) he has a speaking line. So... yeah... whatever Galuf thinks he did back in 2.1 to kill Emmerololth didn't stick.
The very first time Eldibus and Lahabrea acknowledge that an Ascian can be killed is in "Before the Dawn", the very last quest of 2.55. And they are... surprised that something that should be eternal (an Ascian) can be killed. It feels very weird that they should be discussing that in 2.55 when an Ascian Overlord supposedly died in 2.1.
