Hopefully this answer's everyones questions on Lilly from the Game and Lilly from the novel this what Kirkman had to say about it in an interview with playstation.
PSB: Speaking of the novels, I recently finished The Rise of the Governor. And I understand the next book Road to Woodbury will focus on Lili, an infamous character from the comics. Will there be any tie-in to the game? Is there any chance Lili appear in future episodes of the game, for example?
Robert Kirkman: There will definitely be a character named Lili in the game. Whether or not that ends up being the same character we know and love from the comic and the upcoming novel remains to be seen. But yeah, the new novel comes out in October and I’m excited about it. The novel series, the comic series, and the video game all are intertwined in the same universe. Keeping that continuity straight is something that’s been very important to me, and yeah, we’ll definitely see them continue to connect in a lot of interesting ways moving forward.
heres the link to the full interview http://blog.us.playstation.com/2012/08/22/the-walking-dead-9-minutes-with-robert-kirkman/