I can confirm this bug as well. I've lost two highly enchanted diamond swords to this bug, both times while smelting. After interacting with a furnace, they have simply vanished from my inventory. They were slotted on my hot bar.
I now put all my valuable inventory into a chest before interacting with a furnace. I've noticed that some of my remaining inventory will resort itself after using the furnace. My suspicion is that one item gets sorted on top of another, causing the loss of the item. I can consistently get a crafting table to change positions in my inventory whenever I place something into a furnace. Not all items change inventory slots, but a crafting table definitely will.
J.J. Ramirez
MCPE 1.0.2 on Android 7.1.1 (HTC Nexus 9)
I can confirm this bug as well. I've lost two highly enchanted diamond swords to this bug, both times while smelting. After interacting with a furnace, they have simply vanished from my inventory. They were slotted on my hot bar.
I now put all my valuable inventory into a chest before interacting with a furnace. I've noticed that some of my remaining inventory will resort itself after using the furnace. My suspicion is that one item gets sorted on top of another, causing the loss of the item. I can consistently get a crafting table to change positions in my inventory whenever I place something into a furnace. Not all items change inventory slots, but a crafting table definitely will.