A previous game update increased the distance Fane could be from that encounter and still be pulled in (IIRC double the usual distance, or so).
Did you try all dialogue options? If your reputation is high enough there should be an option that always works, while some of the others may be easy, hard or impossible. Just missing that one encounter may not have been enough to get him to always leave. There are choices that will block at least some companions from continuing, even if their opinion is otherwise ok (related to refusing particular points in their personal quests), but I don't know if that is also the case for Fane.
There is a back entrance into the academy, which would avoid the companions potentially leaving. Explore the areas separated by lava flows, south east of the dwarven temple.
