Okay, here's my update after talking with my long time SA at a major US boutique.
She said VCA blue agate is absolutely natural and not dyed, which does make it more rare and desirable than dyed agate. She said changes in any kind of Alhambra stones can be caused by various conditions such as skin and other exposures (such as sun, humidity, water, perfume, sunscreen, etc.).
@A bottle of Red She also showed me a picture of her own carnelian bracelet that has stones with one or two darker stones after wearing it for years. She said some change over time is normal with these natural stones. She said it is okay to clean it on occasion with a damp cloth.
I do acknowledge that I am concerned about those here who have had the fading that is worse than what would be considered normal, and I encourage you to contact your SA. It is very possible VCA just hasn't had many complaints since the BA is a relatively new stone. My SA had not heard of any complaints and I am sure she and her boutique have sold a lot of it. She also checked with customer service.
So I think the key for me is to avoid wearing it outdoors for long in the summer heat and sun. We use air conditioning from now through September, so it is not in danger indoors.