Plot hole: Palmerdale and the others hear someone on the stairs. Skinsale opens the door and, despite Reuben being right in front of him, looks downstairs and calls out to the Doctor before turning and suddenly spotting the lumbering keeper.
Continuity mistake: When Palmerdale wakes Harker up and asks him if he can use the telegraph, Harker answers him, then asks him to repeat the question, then answers again.
Revealing mistake: At the very beginning of episode four, after Vince is killed, Reuben's body breathes and his fingers move.
Continuity mistake: In episode 4, Skinsale is murdered by the Rutan on the stairs right outside the crew room but later in the episode when the Doctor and Leela runs down the same stairs, Skinsale's body is not there.
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