For those of you wondering, I will spell out exactly what happened with Derpy, from a purely factual standpoint.
The Last Roundup episode dissappeared from itunes within a few days after its release, spawning the initial "Derpy scare" a few weeks back.
A few days ago, the episode was restored to itunes, with three changes surrounding Derpy.
1. Rainbow no longer uses her name.
2. Her voice is changed; it's now higher pitched and she speaks more quickly. Rainbow's lines during that conversation have also been re-recorded.
3. Derpy's eyes have been un-derped in that scene. Animators from the show have confirmed that this change applies to that scene only, and her eyes will still be derped in all other episodes.
All these changes, AS OF NOW, apply only to the itunes release. The episode has not aired on TV since its premiere, so it is unknown at the time what will be shown on TV.
The "Friendship express" DVD contains the episode, in which none of the itunes changes apply.
At the moment, it is unknown if Hasbro instigated this change, or if apple did it for the itunes version. Regardless, there are still ways to get a hold of the "old" Derpy scene, and her future appearances as an easter egg character will not be affected.
Also, yes, I do still lurk in these forums, I just hardly ever post anymore.