After setting nbt it clears all current item meta, is there a way around this?

nvm was using deprecated new NBTItem(item, true)

That isn't the issue(NBTItem is just deprecated so people move to NBT.modify/get instead). ItemMeta contains the nbt. So getting meta(contains a copy of the nbt), changing the nbt and then setting the meta reverts the nbt back to when the meta was created.