Try http://www.mediafire.com/?1ih6cxp2g4z9ne0, if on PC? The dead tree should disable if the sapling is enabled. That ought to fix it retroactively, yet still work with a new game.

Better use console commands as described here: http://www.uesp.net/wiki/Skyrim:The_Blessings_of_Nature#Bugs

I've really never noticed that the small tree was hidden within the big old one...