^ I wish compiled code retaining comments even made sense.
John Henry may have been talking about his own code. He did say he and the other AI share parts of their codebase, that's why he referred to it as his brother. The only other system I can think of that contained at least part of the same code as John Henry is the Turk 1.0, which Sarah torched.
Andy Goode worked at Cyberdyne, so that's how code bearing comments from Miles Dyson ended up in John Henry. Recognizing the kinship with his 'brother', John Henry went over his own original source code, and found the comment.