Every time I end up in metamorphosis, either through the ability itself or by way of eye beam with Demonic talent, the Havoc Demon Hunter covenant abilities stop showing up in the rotation.

Edit: This seems to be the case only before choosing a covenant, while the abilities are extra ability buttons and not in the spellbook.

I think this may fall under the heading of "Ovale's default scripts are for max-level characters", or in this case, for characters that have chosen a covenant at max level. The covenant spells from before a covenant is picked at max level are only temporary spells with completely different spell IDs from the max level ones.