Inventory and items not updating properly

My inventory does not seem to ever update properly with items never being removed, or unexpectedly removed. And then the items themselves when modified in game are not actually being modified. I upgraded a dagger and the game thinks its updated, but the inventory does not show any change. In the game the dagger and materials were supposed to have been handed over to the craftsman but never left my inventory and the supposed enchantment was entirely wrong in dialogue, corrected but the item is still un affected