I think it's fine to leave all the other colors unchanged (besides the highlighters, they are visible only until you lift the pen, so maybe it's more an issue of how to render them on dark paper). If you export without background (e.g. if you send your document to someone who prefers a white background, or if you want to print it), white ink is the only color* that won't be visible anymore. Therefore it should be converted automatically.
* as long as you don't add the colors of the yellow and dark paper to the standard color palette.
I think it's fine to leave all the other colors unchanged (besides the highlighters, they are visible only until you lift the pen, so maybe it's more an issue of how to render them on dark paper). If you export without background (e.g. if you send your document to someone who prefers a white background, or if you want to print it), white ink is the only color* that won't be visible anymore. Therefore it should be converted automatically.
* as long as you don't add the colors of the yellow and dark paper to the standard color palette.