The archbishop believes that the only reason why Shirafune would be marked would be if the other side knew he had the data, as alluded to at the end of Chapter 8. However, only the archbishop and Shirafune know that he has the rosary, meaning that, for the other side to know that Shirafune has the data, Shirafune himself must somehow know the importance of the rosary, and leaked that information accidentally or intentionally.