at the end of Final Fantasy IX, Kuja said that the assimilation of Gaia by Terra has already started and the Iifa Tree would incite a Cataclysmic Destruction of Gaia with Zidane's response being that even if that happened the planet would remain and they would make a new home.
after defeating Necron Zidane and party appear at the entrance to the Iifa Tree just as it starts to lash out with it's roots rising up and growing out (some of which turned back into the Tree trying to stop Zidane).
during the "some time after..." part we see
- in Burmecia we Sir Fratley and Freya talking about the rebuilding of Burmecia
- in Lindblum we see Cid and Hilda in the elevator of the Grand Castle with Eiko
- in Alexandria we see that the place has been rebuilt
all 3 places were in the midst of rebuilding (though there was no signs of damage in the Lindblum Grand Castle anyway) and there's no signs or mentions that anything changed regarding the assimilation or damage caused by the Iifa Tree.
so in the end what happened to the Iifa Tree and Terra?