ItemMeta apply is a destructive process that expects to be the authority on
what the items NBT data is.
When CraftItemStack.asNMSCopy was called, the conversion ran, potentially setting
the converted data into the ItemStacks tag.
Then if that item had ItemMeta, it would completely undo that conversion by
erasing the NBT Tag.
On copy, run conversion post ItemMeta apply.
Aikar