Q: Remove duplicate color in Current Fill Flyout Window

I'm trying to add my team's colors to Keynote's color flyout windows. The theme I inherited has one color that's in there twice. If I try to replace one of the colors with a new color, the two identical color squares are replaced with the new color - in other words, these two color squares are linked...whatever change happens to one happens to the other. Here's a screenshot.

I have two questions:

1. How do I break the connection so that I can replace one of the duplicate color squares without it changing the other one.
2. How would I create duplicate color squares in the color picker? I can't seem to recreate this. Let's say I have a blue square and a red square. If I try to replace the red square with the same blue color (to have two blues and no reds) what ends up happening is that the original blue square and the red square swap places.