Audio problem: In episode 3, when the dog is barking at Sam's house and is abruptly silenced (apparently by an Auton), the sound is obviously not a dog barking. It sounds a bit like a man pretending to be a dog, and going "woof woof" not very convincingly.
Audio problem: When the Doctor arrives at UNIT HQ in his stolen car, he speaks to a guard. We see close ups of the guard twice...but watch the brief clip of the Doctor (Jon Pertwee) between the two and you can just see that his lips aren't moving even remotely in synch with the words. (In fact, it is just a repeat of the previous shot of the Doctor, with new lines dubbed in).
Audio problem: The music accompanying the closing credits fades down part way through (at a different point in each of the four episodes) and simultaneously fades up at a different point, the net result being a rather disjointed-sounding edit.
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