Factual error: In Episode 3, Zarof fires a gun. The muzzle is seen and a sound is heard but the gun doesn't move and there's no smoke or bullet, no flash or anything at all. (00:23:05)
Continuity mistake: In Episode 1, the TARDIS crew pass out from the change in pressure as they descend into the Earth. However, at the end of episode four, they climb out on foot and suffer no ill effects.
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