There are two branches of the Special Edition, both based off of the original 1997 Special Edition. The first branch was done in HD, with new (worse) color-timing. The first set of changes were done in 2004 adding more prequel tie-ins, the second set in 2011 adding changes that would be included in the 3D release. The second branch was done from a new scan of the 1997 Special Edition in 4K, redoing all of the changes made in 2004 and 2011, but with color-timing closer to the 1997 Special Edition.
For a great overview of all of the changes made to the movies (including audio) (including the prequels), check out Original Thrillogy on YouTube and the playlist embedded below.