Further info, was using Goblin Axe to cut trees when this happened. It has happened in Terra server but I was watching closer. The stump never appeared when the tree was cut down. (Guess I somehow cut too much wood in one pass and took out the trunk.)
I have managed to almost completely remove 2 of the 3 grand elmore trees from Kasambra Pass. I was chopping them down and suddenly the tree did not re-grow, in fact, the stump has also vanished. The only remaining trace of the tree is the revolving green ring around where the trees should be. One of the missing trees is right outside the Nidaros Mines entrance.