The correct answer is: C. The boss asked his secretary if he had discussed that matter with the manager.
The boss is using the past tense “discussed” because he is asking about a past event. He is not asking if the secretary has discussed the matter with the manager yet, but if he did discuss it in the past.
Option A is incorrect because the boss is not asking if he discussed the matter with the manager, but if he did discuss it.
Option B is incorrect because the boss is not asking if the secretary has discussed the matter with the manager, but if he did discuss it.
Option D is incorrect because the boss is not asking if the secretary has discussed the matter with the manager yet, but if he did discuss it in the past.