Clones are clones. I think there's probably an argument that in some conditions seeds will produce more yield, as they make a tap root and can gather nutrients more efficiently. However, when we grow indoors we give our plants easy access to nutrients anyhow so I can't imagine it makes _that_ much difference in these circumstances.
I think more likely than genetics "degrading" after just a few runs with one phenotype, other changing grow conditions are leading to a reduction in yield. Maybe the temperature is off or the training is different, something that has changed other than the genetics.