Answer: Daylilies hybridize easily so the changes you've noticed probably come from new plants created in your daylily bed. There's not much you can do to prevent this except perhaps to grow only one kind of daylily, or to remove spent flowers before they set seed. If your plants had a virus, the leaves would show symptoms of streaking or mottling. So, as long as the foliage looks healthy, I'd chalk up the color changes to new hybrids.
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