Assuming you did this by copying char_swatches_lit and pasting it in the character's P3D (like this), the char_swatches_lit texture in global.p3d is taking priority over the custom one since it loads the one present in global.p3d first. You should still be able to see the custom char_swatches if you were to make the costume it's own separate skin and make it a purchasable reward in rewards.mfk.
As a quick and easy fix, you'll want to go ahead and rename the char_swatches_lit texture in P3D Editor 4 to use another name, and then change the shader that Homer and Bart use to instead use the new custom name.
Spoiler: Here's a quick visual example:
Note the new texture name at the top and the shader now pointing to 'char_swatches_lit_customhomer'. The name for the new texture is an example and can be renamed to something that's abbreviated and much more pleasant on the eyes.
Alternatively, using Blender to edit the character models should allow you to change the colors of the character model without having to create a unique custom texture for each, but this is perhaps the easiest solution.
Let me know if you need any more help, and do consider Josh's above advice above if you're still running into issues or want to chat!