While the Preeminent Attegoth had been destroyed along with all Skullius' skills the Hybrid Luman retained the ability to control [Evil Darkness] and [Just Light] still.
Skullius did not need skills to manipulate these two elements. Back in the Labyrinth of the Yoke, he had been able to control [Evil Darkness] and [Just Light] before even receiving his first skill related to the elements, before even receiving the legacy.
The reason was, of course, his affinities.
As long as Skullius had a good affinity, he was able to freely control the elements well enough. Skills for manipulating these only added a much-needed finesse and simplified the process. Where additional crutches were truly needed, was for the mass production of elements.