SCC wrote:
In response the the OP's question: The tomb was destroyed as part of a program to erase the actual history of the Seijin's with, well let's just call it a suitably heroic one.
Again, it seems more like a partizan operation of some Archangel (quite probably Chichiro), not the coordinated decision of all remaining Archangels. After all, if they all wanted to erase the true history of Kohdy, why return his body at all?
It looks more like that the general consensus between Archangels was to leave the Kohdy as it was. But someone - Chichiro, probably - was not satisfied with this, and left secret instruction to Rakurai Array and Temple system. The Rakurai Array destroyed the original abbey AFTER Archangels departed, and Temple AI's worked to re-write the Church history, probably by making small alteration to archives over the decades.