She didn't return to reprise her role, though recordings of her from Toy Story 2 were used for flashback scenes in Toy Story 3. However, Unkrich did do one of the additional voices.
To quote the June 2010 issue of Bay Area Parent magazine:
|“||My oldest daughter, Hannah, when she was very little - I think she was 3 or so when we made Toy Story 2 - was the voice of Molly. We have a flashback scene in Toy Story 3, so I went back to the sound recordings. It was heartbreaking to hear those crisp recordings, like it was yesterday when it was 10 years ago.||”|