Things like Primal Earth, Fire, Water disappear when you combine 10 motes. Some people on the official forums have reported disappearing of items from blacksmith.

I myself combined a few motes of earth and the 2 primal earths never showed up. After removing the addon and restarting they did show up with items from previous JC crafting sessions (like 5-6 items from 4d ago).

This was happening to me as well, until I had realized that I had accidentally toggled off one of my bags within the 'Bag Slots' menu.