I think it’s interesting they noted the flowers stopped making the new pigment in the wild after 3 years - is it a genetic treatment that requires repeated intervention to maintain the effect?

I’m also guessing the new genes don’t propagate to the seeds as well, so that they can have a steady demand for their special flowers.

No, the trial was only conducted for three years, presumably because that's how long they budgeted. I don't think they actually stopped producing blue flowers at that point.