Boosting contrast won't help you if you can't tell the difference, so you actually want to shift colors away from the ambiguous axis. This necessarily has the effect of removing certain colors.

Not exactly. It’s not that I can’t see the colors, I just need more contrast to pick up red or green. A grayish green looks the same as plain gray to me. A small bright green dot? Might as well be gray or brown. But a large, solid area of bright green or red? No problem at all.

You can also overlay hints, for example different shadow ditherings depending on color ? Im actually pro ambivalent colors as this is what feels natural for somebody color mismatching.