(SPOILER)According to a response in the Sept. 30, 2008 Behind the Eclipse CBR Q&A, Sylar lost the previous abilities he had gained, except for intuitive aptitude and telekinesis, due to his exposure to the Shanti virus and had to start over in gaining other abilities. The lost abilities would include freezing, enhanced memory, melting, enhanced hearing, precognition, and induced radioactivity. However, Sylar was able to use induced radioactivity and precognition in a possible future (I Am Become Death). In a response in the Oct. 13, 2008 Behind the Eclipse CBR Q&A, it was clarified that Sylar reacquired those powers during the time period inbetween the present and the future shown in the episode.
In other words: total cop-out.
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