The tree he planted in Mzimu Grove got burned down, not the one he actually lives in. That one has to still exist since it's in the latter portions of Simba's Pride.
Fun fact: I actually created the page, but I initially named it "Rafiki's Ancient Tree" before it was called "Rafiki's Tree".
As far as I'm aware, it's never been called the "Tree of Life" in the franchise, but looking at the page's edit history, it was somewhere referred to that somewhere on a miscellaneous Lion King website. However, I don't think it's official.
I do recall somewhere though years ago that Baobab Rafiki lived in on a game or something was referred to as the Tree of Life. Where might've been lost to time though...
After Kion and Ono are injured in an attempt to defeat Scar in the battle for the Pride Lands, the Lion Guard must embark on a journey to the Tree of Life to help them regain their strength.
Lately, Rafiki's ancient magical tree he lives in has been called The Tree of Life officially by Disney, so I just find it silly that like TLG here didn't research that first.