From this comic

More experimentation with Nanase's eye color! As previously mentioned, it was established super early in the comic that Nanase's eyes were green, but I'm not sure that sits right with me. In fact, I'm fairly certain of it. Green and red are complementary colors that create a strong contrast, and it severely limits what sort of outfits can go well with both her hair and her eyes.

Of course, I could have the green be more muted, or adjust her hair color, or a bunch of things, but I think the simplest solution is to take a mulligan on what I established over a decade ago and go with something that works now.

That said, I'm not certain I'm satisfied with this eye color, either, but all of these color schemes are perpetual works in progress in any case.