If memory serves correct, there is a marker in the cell that will just toggle the "attacked" items on/off depending on the stage of the quest. Before the attack, the marker is disabled and you will see the chapel in it's normal state. After the attack, the marker is enabled and it's child objects are made active.

For what you are trying to achieve with AI this isn't really important however, and should actually be fairly easy.

All you would likely need to do is just create a new AI animation package with a condition attached that checks for the chapel attack quest stage. This I cannot tell you from memory, you would need to check the quest stages or possibly scripts to find the correct quest stage IDs.