Hi Melissa, welcome to ATP!
I agree with what Ann says, and though neither of us would say we are experts, our experience is very similar when it comes to how daylilies can take some time to adjust after stress.
You are right that daylilies can cross-pollinate, too, so any insect that might visit two of them could create a fertilized pod by carrying pollen between them. When a fertilized pod dries and cracks, and seeds fall to the ground, new "hybrid" daylilies can grow from those seeds right next to their parents, making it confusing to tell the two apart. It would be easy to get those new daylily fans mixed in and not realize it during a move, after foliage has been eaten, or perhaps moved again to a raised bed.
It may also be possible that they are just performing differently due to changes in soil, weather, sun exposure, etc. Here are a couple of the pictures from the database that Lin was so kind to link to. You can see that, depending on where a daylily is planted, the color can change from very pale yellow to very deep yellow or almost more "gold." And, it may take a few years for flowers to bloom "true to form" after they have been moved or stressed - they can look quite different until then.
Grown in Southeast Texas versus grown in Ontario
With the possibility that you have some cross-pollinated flowers mixed in together, fragrance may be different also.
If you want to keep colors together in your flower beds, but avoid any cross-pollination, you might just want to "dead head" the flowers before they set pods, and clear away any pods that do set - before they ripen and drop seeds.
