Plot hole: The Brigadier says UNIT HQ is 'a Top Secret establishment'. It is, in fact, so secret that it has a large sign outside informing the world not only of its function, but also the name of the commanding officer.
Plot hole: After UNIT HQ disappears, you can see a patch of grass where the UNIT HQ used to be...but just exactly how can grass grow underneath a building?
Plot hole: Professor Jones says they tried to borrow the cutting equipment a few weeks ago, but Mr. Stevens says it was yesterday. One of them must be wrong...
Plot hole: Jo should know what the dematerialisation circuit looks like. She saw it in 'Terror of the Autons', 'The Three Doctors' and several other episodes.
Plot hole: 10,000 Daleks sounds impressive but it wouldn't be enough to invade a planet, let alone an entire galaxy.
Answer: It was never destroyed on-screen; it was intact at the end of the TV movie, and destroyed by the start of the 2005 series. It was destroyed in the novel "The Ancestor Cell," but in a completely different manner to what happened in the series.
DaveJB