Deleted Scene: The author actually included two endings in a particular chapter. One suggesting Ulquiorra had betrayed the ponies of his own volition, the other stating he was actually brainwashed the entire time.
Chapter 43 contains a deleted dance scene.
Chapter 64 had a deleted scene on why it was that Equestrian ponies could vomit, but the ones from our world couldn't.
Chapter 67 has a deleted/extended scene with Ulquiorra going into much greater detail with insulting Thrush, clarifying to Celestia what "shithead" means, and ending with physically throwing Thrush out of the room because Celestia asked him to.
Chapter 72 gives a different take on Rainbow Dash's argument with the voice in her head.
Deleted scenes show up nearly every chapter now.
Reality Subtext: According to the author, chapters 66 through 67 supplemental were written in response to the Justina Pelletier incident.