This is very similar to SPIGOT-4935, but I'm not seeing JSON in the lore, I'm seeing no lore at all when loading old (pre-1.12) items.

Here is an example of an item saved pre-1.12:

item:
  ==: org.bukkit.inventory.ItemStack
  type: WOOD_HOE
  damage: 14
  meta:
    ==: ItemMeta
    meta-type: UNSPECIFIC
    Unbreakable: true
    display-name: §aLightsaber Hilt
    lore:
    - Used to construct a Lightsaber 

This item loads mostly correctly, except for the lore which does not show up in-game. I think maybe it's not being converted to a ChatComponent on load?

I've attached two screenshots, one showing the lack of lore in-game, and another showing a raw NBT dump showing that the lore is there, but in plain text instead of a ChatComponent (like Name).

I can provide an example plugin if needed.