I think they have certain routing rules in addition to normal award rules. When ZRH-JFK nonstop was dropped, I was not allowed ZRH-PHL-LGA(or JFK) initially as it was not a route permitted to get to New York(although it was showing as Saver award). I informed them that the nonstop is no longer scheduled and hence it should be allowed. After a hold of few minutes - the agent said she verified and indeed it can be done.