Frankly, we’re surprised at how many eagle-eyed readers have noticed this. No, you didn’t miss anything: that is the only reference to said eyes in the novel. And it only appears in the paperback version, not the hardcover version.
What you have discovered is the seed of a sub-plot, or complication perhaps, that was developed after the hardcover was published and that affects Agent Pendergast’s life to one degree or another in all future books. There are other, equally brief, allusions to all this in Still Life With Crows. This sub-plot, however, truly begins to develop in the ‘Diogenes trilogy’ consisting of Brimstone, Dance of Death, and The Book of the Dead, and of course the Pendergast novels that follow.