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Centerpoint Station was destroyed during a battle during the Second Galactic Civil War in which the Jedi reprogrammed it so that all galactic coordinates were equal to its own, so when the Corellians fired it, it destroyed itself. I think you're conflating this with the mission that Jacen and Ben went on to Centerpoint in Betrayal, which didn't result in its destruction.
There's also the insinuation that Abeloth's release was merely a consequence of a succession of several wars: the Clone Wars, the Galactic Civil War, the Yuuzhan Vong War, and the Second Galactic Civil War, and the destruction of Centerpoint was merely a catalyst but that her release was inevitable.
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