From what I can see in the cinematic, I don't think Baldur's Gate got "destroyed". There was an attack, there was some damage, quite a few people were abducted. But overall not a "destroyed city". The Nautiloid was in the city only a short time before it got chased away by the Githyanki.
The city is not baldur's gate, it's another city. Swen mentioned it in a stream but I can't remember the name.