In SuperChargers, the Dark Rift engine was recovered from the Vault as a last resort to defeat The Darkness after the Core of Light was destroyed. Successfully activated by Kaos inside the Sky Eater, it consumed the entire fortress and The Darkness, and was presumably destroyed with the rest of the Sky Eater after The Darkness was defeated inside the Rift.
Despite being sealed away thousands of years ago by the Ancients, The Darkness knows of its location, to the point of speaking about it in its sleep. This is also inconsistent with the time it was used by the Spell Punks, because Pluck never refers to an attempt to steal it or the Rift ever being put back on its resting place.
The Dark Rift Engine is different from the Dark-elemental Rift Engine used by Nightfall, which has a normal size and no difference in coloration.