I have a book where the hero's eye color subtly changes three times but not until much later in the story does the reader understand it is not a mistake but a surprising part of the plot.
Should I inform the publisher that the eye color is NOT a mistake before they start to read it? I had one editor claim to have carefully read my manuscript then proceed to made a harsh/nasty comment about my unprofessionalism with the eye color. I didn't respond and explain myself because I thought if they had carefully read it, like they claimed, they would have realized it was part of the plot.
And if your manuscript is rejected with a personal letter from the editor, CAN you contact them and explain yourself? What do editors think about calls like that?
If the editor noticed the eye color change at all in the first read, then they were reading carefully. I can pretty much guarantee that if everything else in your manuscript was spot on, you would not have been rejected for unexplained changing eye color, even if it was unintentional. The editor would have simply instructed you to go back and fix it.
However, if there were multiple places where your writing was vague or sloppy or not working for some other reason, they may have assumed this was just one more piece of evidence that the MS needed more work and stopped reading before the explanation of the eye color change was given.
No, I would not suggest that you contact the editor to explain yourself. If the eye color change was too subtle for your editor, it will be too subtle for most of your readers too--and you wouldn't be able to call each of them and explain yourself. And if your MS requires an advance explanation that this is not a mistake, then your published book would require the same advance explanation.
So, use this as a learning moment. Go back and do some foreshadowing so that when the reader hits the first eye change, they have a clue that something unusual is going on. You don't have to give them the whole explanation for the change, but they need to have enough information that they know it is not a mistake. If you pop something entirely out of the blue at the end, the reader feels cheated or taken advantage of. But if it's well prepared through subtle, but recognizable hints, then when you unveil the surprise at the end, it resonates and they are more likely to accept it as plausible and think that you are a really cool writer.