In the Nether, unstackable items inside an unpowered hopper chain or other device that uses hoppers may randomly disappear when they are transferred while the chunk is being unloaded. The disappearing is not a client-side glitch, the items also disappear from the world files stored server-side. One way to reproduce:

1. In the Nether, place two hoppers facing into each other.
2. Place an unstackable item in one of the hoppers. It will bounce back and forth between the two hoppers.
3. For a greater chance of this happening, use multiple hopper pairs with items.
4. To see the results more easily, add comparators to the hopper pairs.
5. Unload the contraption (for example by leaving the Nether through a portal, or by moving out of the area), then come back to it.
6. You will see that some of the comparators have stopped blinking, because the items in these hopper pairs have disappeared. If this does not happen right away, try unloading/reloading the contraption multiple times and/or adding more hopper pairs.

This issue is very likely related to the duplication bug MC-15019 (and was indeed found while exploiting that bug). Items seem to randomly duplicate, disappear, or stay as is.