So yeah, here's a screenshot of what it looks like. http://postimage.org/image/ktbqkjsnp/full/

As you can see, the new sapling is clearly growing inside the old dead tree. From what I understand, this isn't supposed to be happening and the older tree should have disappeared. I figured eventually it would take the same shape as the dead one so I didn't think much of it, but yeah that doesn't seem to be happening.

Yeah, this is a pretty old bug. Try this: first save your game, then open the console and click on the big tree and enter:

disable

In case is doesn't work; try this other command on the big tree, after doing another save:

markfordelete

Save your game a third time and reload it; the big tree should have disappeared and the small one should be still there, unless you made an error on clicking (this is why you must have several saves available so that you can try again).