Sometimes when I smelt large quantities of ores a lot of it disappears ,unfortunately I don't have any evidence to provide  but it has occurred on 3 different occasions
1.smelted a stack and a half of gold and only received only a stack using blast furnaces
2.smelt 2 stacks of iron using furnaces and blast furnaces but only got a total of 36 iron
3.Smelt 1 stack and a half of iron using blast furnaces only got total on 32 iron ingots 

Hopefully this is patched as its quite frustrating.

Thanks