The key is changed, in other words the pitch of the songs is different. Emily's vocal range sits higher than Chester's, so she can't hit the lower notes that he can. Some songs have a drastic change, like Somewhere I Belong, which was originally their lowest tuned song at Drop A# (I think, someone correct me if I'm wrong) and is now being played in Drop D or Drop C#, about 2 1/2 or 3 full steps higher than original. Some are less drastic, like Faint, being played a half step higher than original. That being said, some songs are played in the original key, like Lying From You.
The benefit is that Emily can sing the songs easier, as the vocal melodies fit more comfortably within her range and she doesn't have to strain to hit the lower notes that are out of her comfortable range. A lot of bands do this, however they usually lower the key of their songs so they don't have to strain to hit higher notes. LP did this at the tribute show when Oli Sykes did Crawling. This is a rare instance of a band raising the key of the songs, hence why people are so thrown off by the changes.