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 new sub-plot, or complication perhaps, that was developed after the hardcover was published and that will affect Agent Pendergast’s life to one degree or another in future books. There are other, equally brief, allusions to all this in Still Life With Crows. This subplot only truly begins to develop in the novels that follow: the 'Pendergast trilogy' consisting of Brimstone, Dance of Death, and The Book of the Dead.
We can understand your wanting to know more. But realize that in so doing you run the very real risk of spoiling your own surprise!