I enjoyed the story btw, I was just confused by that detail.

Okay, so I rewatched both End of an Era and A New Beginning. In A New Beginning, Thancred is definitely in the Ossuary in the post Calamity portions of the video. You can't really tell which statue it is in End of an Era because of the blue light. The juxtaposition of the two halves the video work to suggest Thancred is in the Ossuary during the calamity, but technically it could have been the Sacrarium.