If you serialize a chest with ItemMeta into yaml, save the config, reload the config, and finally retrieve it, the chest will have lost of of it's ItemMeta. Example chest "54:0 1 Unbreaking:1 name:&9Test_Chest lore:&5Serotahu"

This plugin is the simplest to exhibit the bug https://github.com/pascoej/ItemSerializationBug

Or if you run this code:

saveDefaultConfig();
ItemStack itemStack = new ItemStack(Material.CHEST);
List<String> lore = new ArrayList<String>();
lore.add("test");
ItemMeta itemMeta = itemStack.getItemMeta();
itemMeta.setLore(lore);
itemStack.setItemMeta(itemMeta);
System.out.println(itemStack.getItemMeta().getLore());
getConfig().set("test-item",itemStack);
saveConfig();
reloadConfig();
itemStack = getConfig().getItemStack("test-item");
System.out.println(itemStack.getItemMeta().getLore());

It outputs :
[20:42:17 INFO]: [test]
[20:42:17 INFO]: null

Showing that the lore is not preserved.