The calls are irrelevant, since as Shitt noted, comms could have been done face to face. Trump Jr probably did communicate to his father he had Hillary dirt involving Russia coming, but didn't mention meeting: 1. Plausible deniability; 2. Common corporate practice of not overloading with details. This is why Trump made announcement of forthcoming dirt. Comms after, by whatever means, were that Don Jr had come up empty, with no reference in that context to a meeting (same reasons). This is why Trump cancelled that announcement.
Most likely the meeting was referenced in some vague way at some time, but in context of Magnitsky. Trump noted when the story came out he recalled Magnitsky being a topic at the time, and wondered himself if he had had some knowledge. Call it "fog of war."
