I noticed if I selected to reverse engineer a nanite and then cancelled the action the nanite just goes away. This happened a few times when I had already started the action and so I figured it was working as intended. However, just now I had a whole line up I was setting up while the game was paused and then realized I needed to do something else and started cancelling them and the pile got smaller. I thought maybe it split the pile so I searched in the inventory and they were just gone!