She died. We do not know how, but in Chapter 425, when Kakashi was about to die while fighting Pain, he is thinking to himself. He apologizes to Obito for not being able to protect Rin. Then he says the he will be with them soon. "Obito...Rin...Master...I'll be there soon."
well when kakashi was fighting pain and he was close to death he mentions im sorry obito about the promise i made you i couldn't even protect rin so that shows that she died. how she died hasent been confirmed