The mythical Blade affinity…
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One of the things that the skill system does is change how icons work to support skill icons, and in doing so enables separating different kinds of icons onto their own sheets rather than needing to share one with item icons. You can edit the image it references for affinity icons using the patch IconRework AffinityIcons(Requires Skill System Patch). It seems that the patch won’t allow you to increase the size of the image, but if you were to insert an uncompressed extended icon sheet image and repoint the image to your new one it should work correctly. Because which icon is used directly uses the affinity ID, there’s no need to link them together in any other way than putting them in the order you want.