Bug! As of patch 1.04, if you purchase a remarkable amethyst while having regular ones in the inventory, it may become a regular amethyst or disappear after you exit the merchant screen. If you sell all regular amethysts before leaving the screen, the bug will not be triggered.
Bug! As of patch 1.05, even if you avoid triggering the above bug, having the remarkable amethyst in your inventory when choosing to give amethysts to the dwarves via the Allied Supply Crates will result in the remarkable amethyst being given away as well.