Continuity mistake: After Skagra demands the book from Professor Chronotis, as Skagra's sphere floats toward Chronotis he's wearing his eyeglasses, but then the Professor's eyeglasses vanish and reappear while his hands are raised.
Continuity mistake: During the animated portions of Shada's missing scenes, in numerous shots an illustrated character's clothing (buttons, scarf, etc) become flipped, sometimes even within the same shot. Example: when The Doctor goes to the physics lab and meets Clare Keightley, note her buttons and The Doctor's scarf.
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