I got the impression that Apollo had been lost and returned once (OK I can think of a few times, most involving lightships
that this happened, but that the Adama log at the beginning was to be heard by Troy, only if he succeeded Adama as Commander of the Galactica. It also implied Apollo died or went MIA when Boxey was very young still. (I got miffed at Glen at this point, glad the books are not Canon for this issue if no other reason!)