Plot hole: When the Doctor goes into the CET projection of Eden, to fight the Mandrells, he disappears into the bushes on the left-hand side of the screen. Cue much shaking of foliage, and Tom Baker's cries of 'ooh', 'aargh' and 'ouch'. The Doctor then reappears with his clothes all tattered and torn, due to his 'fight' with the Mandrells...but the the fact that there is not a mark (not even a scratch) on Tom Baker is something of a giveaway that all Tom Baker did was disappear behind some bushes and do a quick change into a tattered version of his costume.
Plot hole: When Della gets shot in the face in episode four, she clutches her stomach. (What is even more remarkable about this error is that this keeps happening over and over again: someone gets shot and falls to the ground, clutching their stomachs, regardless of where they have actually been shot. See the error in Season 14's 'The Deadly Assassin' for an example of the SAME error occurring).
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