I am raging so much for this! I was lagging and spamming shift + right click on smelter to add the charcoal, without thinking that in the same way, if you have not an item in the cursor, you take all the items from the smelter! So, what did happend? The ores were at 99%, and now I have to restart the process!
I think there should be some way to prevent things like this, shift + right click is useful in both situations, but it should not cause issues like this one!