This happened to me in the past 2 days, I lost 90 god apples. I know whats happening. When you go to place them in your inventory, then put them back, and then close your ender chest really fast then there gone i just experimented . Kubsz Or Dan please read
Click all around your inventory in each slot and they might appear. It happens with lag and if you do that really fast you are pretty much creating the lag. It's a rendering glitch.