Ok, finished up BLM AF Story tonight... maybe...
After you get the Earthen Charm from Kupipi you have to again travel to the Rose Tower and pass through the Mage Gate. The Earthen Charm does not allow you to pass through the gate, you still need three mages or the gate pass to do this.
After you are through, continue to the room where the Wendigo's are and go down the North Eastern hallway where the Earth and Water Gates are. Click on the Earth Gate and the Earth Charm disappears.
The three Magi then follow you in the room where you discover a new twist to the plot of the tree.
It does lead you to believe that perhaps eradicating the magic crap in Toramai Canal wasn't the solution. That there is more to this story because the tree knows it is indeed in trouble...
Could this be tied to some other BLM only quests? If you find out please post reply.