I thought mine disappeared also but I found that when it is charged it shows up under miscellaneous sorting but when it is empty it only shows up if you show all in the inventory and on top of that once used it can change to another companion on its own.
The empty one should show in materials/ingredients.
It will only transfer during crafting to a companion, if the recipe is using their resurrection scroll, that means material in their inventory. It happens when I'm crafting arrows and using arrow shafts in Ifan's inventory, he gets the final product everytime.
