Skullius' second mana core, the Nature-Bound Malleable Form Core, was quite unique. Back when Replicus first acquired it, by using [Unbound] on his mana, he had discovered that the core's Refinery did not have a fixed pattern, but was adaptable. It was constantly changing, reacting to its surroundings as best as it could.
As for what a Refinery was…
It was the complex pattern currently revealed from Replicus' mana core.
In essence, what the Penetrator had just done to this second, less vibrant mana core, was to remove its Shell, revealing the layer beneath.
A mana core was like an egg. It was comprised of three parts; the Centre in the innermost part, the Refinery in the middle, and the Shell as the outermost layer.