Plot hole: In the middle of chasing the Doctor, Stor abandons the idea of controlling Gallifrey in favour of destroying it for no readily apparent reason.
Continuity mistake: When the Doctor shoots Stor with the De-Mat Gun, the flash starts on Stor's left-hand side, engulfs him, then jumps substantially to the right before whiting out the frame.
Plot hole: Leela's decision to stay with Andred is very sudden. They barely speak during the serial.
Continuity mistake: The Doctor has his scarf when he first meets with the Vardans. When he returns to the TARDIS, it is on the coat rack.
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