Simple question: is twice in one chapter too many times to draw attention to a character's eye color? It does further the plot in the way of demonstrating the protag's attraction to this character, since she is distracted by his eyes. (Hopefully its less cheesy in the story than it sounds here.) The first reference is her simply being distracted by the attractive color of his eyes. The second is not so overt- just mentioned in some other description of him. Both feel important to me, but I just don't know. Thoughts?
Twice in one chapter doesn't sound like too many to me (Unless it's a super short chapter). And if it matters to the plot then it's completely fine imo. When it comes to descriptions it all comes down to what is needed for the plot. Sometimes you need to being attention certain details, so you repeat them or put emphasis in them in some other way, and some times some details don't matter at all in which case you don't include them. In your case the color of the guy's eyes do matter so it make sense for you to bring attention to them. Now if you go overboard with it and bring up his eyes in every other sentence, then yes it'll get annoying. But twice in a chapter in this context works just fine, imo at least .
If there's a reason for it, I think it's fine! Her being distracted seeping into the narrative also getting distracted pulls the reader closer to the character (at least theoretically). There's a point where it would get annoying, but it sounds like you're well off from that to me.
seems like you're overthinking it a little twice isn't too much, and it also depends on how much emphasis you give to the description. If it's twice in one chapter but both times you spend an entire paragraph on it, for example, then yes, too much. If it's mentioned in passing, then nope, not too much. Another thing is, when unsure, you could always leave it in for now and remove it when you come back to edit, when you've had some distance from your work and can see more clearly.
Normally, it would be silly, but it sounds like you've found a very reasonable exception. What's interesting to me isn't the description of the eyes, but rather that the MC is looking directly into them. It's intimate and shows a certain longing. What would happen if the guy sees the scrutiny? Maybe you're in the description, she's been caught up watching him and being wistful, and suddenly realizes he's looking back.
I think that's the kind of thing you could trust to beta readers after the book is polished, edited and in the best shape possible. If a couple of them tell you it was a good artistic move, or that it sounds repetitive, you'll know. I don't think you can really know yourself. I know I can't.
I don't think it's inherently a problem, no. I do find offhand references to descriptive elements more distracting than direct ones. That is, the "not so overt" one may be the more problematic.
I'm pretty sure I've done that myself a whole bunch of times, and I've never had my editor call me out over it. So my guess is it's fine.
In the original version of my fantasy series, the MC had black irises. As a child she was told that the 'eyes are the windows of the soul' and that 'she doesn't have one'. Since then, she started wearing her hair down in her face (which would draw attention too). So, the eyes and her behavior would come up, especially when she met new people. I tried to stay in the heads of the characters in the scene, what they would notice and why. The story of why she wore her hair in her face didn't come out until late in book one and proved to be a very satisfying scene. Godspeed!