Presumptively this referrs to John Warner, who would most likely have been the SecNav when Kerry was supposed to have received his discharge.
But a SecNav seldom is up to speed on the discharge of every LtJG who musters out on his watch.
But, Kerry called a lot of attention to himself in ways quite inconsistant with his standing as a commissioned officer, so the situation might have been a point of discussion and notice by SecNav.
John Warner would have had sources. As a Senator and as a former Sec of Navy. Come to think of it, if Kerry's Honorable Discharge came in the Clinton administration, you would think somebody would have known the truth -- and that it would have been common knowledge at the time that Kerry entered Congress.
Nixon was up to speed on Kerry.