Oddly enough I had something similar happen, but completely unrelated to the blue essence transfer. I got 1 purple gemstone out of a chest a few months ago, didn't have any immediate use for it but though "Oh, neat." Then later on it showed the gemstone icon but showed "0" for the quantity.
I assumed I used it by accident, but I can't imagine what I would've used it on. Though I always wondered if the Omega Teemo icon thing required a gemstone to craft, cuz I unlocked that around then. But it would be horridly stupid of them to require a gemstone for an event icon (especially one that's kinda eh), so I'm really not sure what happened to it. I never submitted a ticket because I didn't have much use for the gemstone in the first place, but maybe I should.
Or maybe gemstones just evaporate if you fail to maintain eye contact.