When I go to a singleplayer world and spawn a tool/armor with meta data -30000, like /give mihko9 314 1 -30000 (to increase durability) and the rename it to anything, it will eventually disappear from my inventory when you move the item around your inventory and opening an furnace/chest/anvil/crafting table.
Steps to reproduce:
1.Open a world with cheats enabled.
2.Do /give username 314 1 -30000 a few times.
3.Rename all items(in this case golden helmets) to anything.
4.Randomly open/close chests/furnaces/anvils/crafting tables and move the items around your inventory and they should disappear.
Closing this issue since it's now impossible to get something with a negative data value.