To replicate:
When Enchanting:
Make sure 1st enchanting slot is used:
Shift Click another item that can go to that slot.
The item disappears forever.
VIDEO OF THE BUG: https://www.youtube.com/watch?v=xS2LwL-x4SY
MC-89005
1.9 Snapshot Enchanting/Brewing Items Disappear
Resolved
Duplicate
0
A. Felipe Cabargas
(Unassigned)
Unconfirmed
Minecraft 15w38b
Retrieved
Thank you for your report.
However, your ticket has been resolved as a duplicate.
This issue has been linked to the original bugreport: MC-88929. You can find or add further information on that report.
Please search before reporting any bugs, as it's likely that one exists already.