For that exact reason I actually wasn't using the blacksmith upgrades, nor the easy craft option or the free engraves. I WAS using the unlimited arrows option - which is what seems to keep items in your inventory from being consumed, nor crafting materials. I suspect its that one, and upon closing the game when it syncs the game with uplay (in my case) something isn't stored correctly. Thats the only thing that would account for even old manual saves having the item missing now upon start without the trainer even being enabled or even executed.
Same here !
As i mentioned the page before the inf ammo/arrow option breaks quite alot of things.
I stopped using it and just craft arrows when i need them.