Here's the 'evidence' that the Qui-Gon scene was filmed:
First, USA Today reported a brief snippet from a movie premiere comment:
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Star Wars alums Neeson and Jackson both offered hints that George Lucas has shot a top-secret cameo of Neeson as Qui-Gon Jinn's ghost, à la Alec Guinness, for May's Episode III: Revenge of the Sith. "I can't speak about it," Neeson joked. "Jedi code of ethics."
Later, in THIS article from USA Today, the following was said:
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Although his stately Jedi master Qui-Gon Jinn was a goner in Star Wars, Episode I: The Phantom Menace, Neeson puts in a ghostly appearance in the series finale, Star Wars, Episode III: Revenge of the Sith on May 19.
In Phantom Menace, he mentored Ewan McGregor's Obi-Wan Kenobi and trained Jake Lloyd's Anakin Skywalker as a junior Jedi before meeting his fate in a saber duel opposite the vicious Darth Maul.
But much like Alec Guinness' Obi-Wan in the first trilogy, Qui-Gon's influential spirit lingers on.
Then again, not that IMDB is a definitive source in all cases, but their site does NOT list ROTS under Liam Neeson's profile. So I suppose we'll have to wait for the DVD to find out if that scene is included.