Revealing mistake: In episode three, when the root attacks The Daleks in the mining area, the string holding the root up can be seen.
Revealing mistake: During episode three, in the mining area, just before the city's root appears, the tracks on which The Daleks move can be seen.
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