I'm not sure if this was a fluke, or if it has happened to others.
I was deconstructing some items today, with my small ingredient bag open and set to auto-gather. When I deconstructed and the essences were created, the essence stack sizes in my bag didn't change. The essences didn't appear in my inventory or tiny ingredient bag, either. My tiny ingredient bag was also set to auto-gather, but only had dragonshards in it.
Could having both bags set to auto-gather end up preventing deconstruct essences from being put into a character's inventory, essentially deleting the created essences?