I looked in the "Making of Revenge of the Sith" book in Barnes & Noble the other day and it looks like both Shaak Ti scenes were shot. The scene where she is killed by Grievous was shot during principal "photography". It looks like they decided to scrap that scene in favor of the version where Anakin kills her, because there's a part about that in the section about post production. There were images from both scenes in the book.