When the Wrath of Khan belt and badge are equipped in the tailor, the color selection for both of these items are connected in such a way that if you change the first color option for either belt or badge, it changes the first place color selection on the other. The second place color option on the belt and badge are also linked. The only way I have found of working around this is to equip another belt, usually the Jupiter belt, then I can freely edit the Wrath of Khan badge colors without it affecting the Jupiter belt, then I can edit the Jupiter belt colors and when I change back to the Wrath of Khan belt, the changes I made to the Jupiter belt stay with the Wrath of Khan belt. But if i open up either the first or second place colors on either of those belts again, then re-link and the belt colors usually change to match the badge colors. If I don't select a new color and just click outside of the color palette without making any changes at this point, then the belt colors revert to what their desired colors.
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A common fix for linked colours is to use the randomize feature on one of the uniform parts, which seems to break the link.