I came to realize that when saving an ItemStack to YAML, the black color code is not saving to yaml.

Example code:

ItemStack itemStack = new ItemStack(Material.STONE);
ItemMeta itemMeta = itemStack.getItemMeta();
itemMeta.setDisplayName("§0BLACK NAME");
List<String> lore = new ArrayList<>();
lore.add("§0BLACK");
lore.add("§aGREEN");
lore.add("§bBLUE");
itemMeta.setLore(lore);
itemStack.setItemMeta(itemMeta);
player.getInventory().addItem(itemStack);

In this code, I am giving the player an ItemStack with a black name, and 3 lines of lore, coloured in black, green and blue. the black color codes are not saving to yaml, example of how it appears in yaml:

item:
  ==: org.bukkit.inventory.ItemStack
  v: 2230
  type: STONE
  meta:
    ==: ItemMeta
    meta-type: UNSPECIFIC
    display-name: BLACK NAME
    lore:
    - BLACK
    - §aGREEN
    - §bBLUE

As you can see here, the black name and black lore do not have their color codes, but the green and blue do.

Im including my tester plugin so you can try this yourself.
Run command `/test item` which will give you the item
and then, with that item in hand, run command `/test save` which will save to the yaml `plugins/TesterPlugin/config.yml/`