These are some hypotheses I just thought of on the spot.
1. Maybe Rin got kidnapped again but this time by Orochimaru (since he abducted 60 kids)
2. Maybe it has something to do with Kakashi leaving anbu, perhaps he was given a mission that conflicted with his friendship with Rin, sort of like a repeat of what happened with his father, he probably chose the mission over Rin therefore Rin died.
3. (in relation to the first two) Maybe Kakashi arrived too late to Rin's rescue and she died/disappeared.
I could think of more but w/e.