The Yied Shrine is one of the three castles that are in the Yied Desert, and it has long been where the Lopto Sect has hidden in order to avoid persecution. It is assumed that most of the Lopto Sect that appears in Genealogy of the Holy War and Thracia 776, including Manfroy, originated from here. After the Isaachian-Grannvaleian War, the Balmung of Isaach is placed in the Yied Shrine.
In Chapter 7, the Yied Shrine is reclaimed by Seliph from the command of Kutuzov. Seliph is shocked that the Lopto Sect hides under this ruined place, and doesn't think its right that they should have to just because their ancestors were part of the Lopto Empire. Lewyn explains the people would have been burned at the stake if they had not, and that you have to be careful when placing labels on good and evil, and continues to say that you should never waste your anger on individuals, and always focus it on the evil within ourselves.
In Fire Emblem: Thracia 776, it is said that the people that Veld turns into stone are moved to the Yied Shrine, which also supposedly includes the captives of the Battle of Belhalla.