When Weyoun ordered that each city on Cardassia Prime be destroyed as long as Damar and the other Cardassian's persisted on rebelling against them, it seemed that Dominion Headquarters was also damaged.
You'd think that since the building was Dominion Headquarters
that they would some how avoid hitting that structure and just destroy everything else around it. But, I guess it was too difficult for the ships not to hit it since it is close by to the surrounding structures. Just a little something I found to be odd. Maybe the main control room of Dominion Headquarters was deep in the bowels of the structure so that it would be able to sustain heavy damage on the exterior. However, I always thought the main room was located at the top of the structure, or at least near the top of it just as ops is located on the top of Deep Space Nine. Who knows. But why even take that chance and not leave the building untouched? Strange.