Does yolk colour affect egg quality, flavour or nutrition?
No. The colour of the yolk is influenced by the hen's diet and is not an indicator of freshness and has no significant influence on nutrition or flavour.
Specifically it is from plants rich in Xanthophylls, which are yellow pigments from the carotenoid group. Xanthophylls is literally Greek for yellow. Free range egg farmers cannot depend on pasture alone to deliver a consistent yolk colour and so most will add supplements to the feed. We include very low levels of natural plants extracts derived from Marigold petals and Paprika in their diet. This is not intended to create a false colour, but simply to achieve a more even result. These extracts contain the same natural Xanthophylls (lutein) that would normally colour the egg yolk.
But our hens are not machines, so there will always be variations in yolk colour that are beyond our control. What's important is that their diet is regularly monitored to achieve the best nutrition for the hens. And in turn you can enjoy nutritious healthy free range eggs.
Even the RSPCA ackknowledges that yolk colour does not affect the nutritional value of the egg, and is not influenced by the type of production system in which an egg is produced.