I suspect that the Kaylons changed his eyes to blue to make him appear more friendly and less threatening as part of his mission to collect data when he was sent to the Orville. The Kaylons probably also altered his personality somewhat to make him friendlier, A) to hide their true intentions and B) to make it easier for him to do his mission. In essence, it was part of his cover. I think there was even a little hint about this in this episode where they mentioned that the red eyes make them look very threatening or something to that effect. When the Kaylons reboot Isaac they keep his eyes blue so as not to betray the fact that they changed his personality back to "evil kaylon". Issac did seem a bit out of character after the reboot. Before, he had a huge superiority complex, sure, but he was still somewhat agreable with the crew. He was nice to Claire's kids and acted like he wanted a real relationship with Claire. After the reboot, he throws away the picture and acts like a total jerk. Now, maybe it was all an act before. Or maybe his deep cover personality actually became real. My theory is that this will play a role in next week's episode. The crew, maybe Claire, will realize that Isaac is not acting like he used to and will realize that the Kaylons altered his personality. The crew will find a way to alter his personality back to the way it was, and Isaac will help them defeat the other Kaylons. Ultimately, I think the eye color is meant as a quick visual hint to the audience. Red eye Kaylons are evil, blue eye kaylons are good. It would be interesting to see if we meet any other blue eye Kaylons who don't agree with the "exterminate all biologicals" directive.
