Destiny of the Daleks - S17-E1
Deliberate mistake: The shot of the alien spacecraft flying in the sky is the same in episode 4 as in episode 1, only it's reversed. The taking off and landing are the same too, except smoke and rubble have been added.
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