Cities Protected by Unfinished Military HQ

[Deantwo]

I don't know that we figured out a way to identify it prior to destroying it.

Simply look at the Building window's Building tab while you are at the building's site.

Also, in the past you could still shoot underground buildings from orbit.  That is no longer the case.

Crew will not fire at buildings that are blocked by terrain. You can manually use a missile launcher weapon bay to dig down to the building, once it is dug free a crewman manning an energy weapon bay can shoot it.

Welcome to my hell.