You found a hole in the quest programming logic.
There are actually two copies of the emeralds. Prism has one set, and the other set is in the eyes already, but the containers are disabled.
* If Prism goes red-circle, the set in the eyes are destroyed. You kill Prism and get his set.
* If you let Prism finish his masterpiece, his set is destroyed and the containers are enabled. You loot the eyes from the statue.
So, by having Prism go red-circle and then letting him finish his masterpiece, you managed to destroy both sets. Whoops!
To complete the quest, you'll have to create the emeralds via the console: