I feel like this is working as intended. When you level sync on a particular class, you are no longer that level for that class only. In the case of Conjurer/whm, you don't get Stoneskin because you're no longer at the level to use it. If you have it set as a cross class skill on your Arcanist and level sync, your Arcanist level goes down, not your whm so you will still have access to the skill.