Yeah that color blindness issue certainly pops up from time to time and I imagine that it is enforced at times, where appropriate. A doctor may not necessarily just sign-off. But if you really didn't hear that, it may be worth a try.
It may not just be the Navigation aids that are so important: many of them are shaped and numbered to distinguish them uniquely. But I know that I need to distinguish between green and red lights at night to be able to determine whether that freighter over there, is coming or going. And if it is coming, to know which way it will cross my path. I am not a certified Captain but I would imagine that is the critical skill that must be consistently demonstrated for qualification.
I had my first experience a number of years ago where color vision was important. We hired a part time guy to help out on Printed Circuit Designs. It turned out that he was asking which pen to put in our old "single pen" plotter. I said, when the plotter prompts for pen1 to put in the red one and prompt for #2 is the green one, etc. "Which one is the red one" he asked? The pens themselves were not numbered but plainly colored for those that could distinguish the sprectrum. Oh, that one caught me by surprise... it turned out that he was never assigned to the task to check the paper plots. That was not a good job assignment for him based upon his abilities.
I recall going through vision tests at Homestead Air Force Base a number of years back. The color vision tests involved holding up cards, usually with a large number or letter blended into an array of dots. You did not have to guess the color, per se; but you did have to successfully distinguish the pattern that was on the card. Some cards were so subtle in contrast that I could imagine that with a color vision deficiency that character would be invisible.
One suggestion that may help is too practice with the testing mechanism. I worked with another colleague that was also color blind in some areas but he was still able to distinguish "a difference" between two choices. You may just need to develop a bit more sensitivity to distinguish and perhaps can overcome this requirement. Good luck with the next go round.