why would you need to destroy anything if there's pardons involved. Even if they have the proof you committed wrongdoing, the pardon means you suffer no consequences.
To prosecute people guilty of state-level violations (which are not covered by Presidential federal-level pardons). To find 'collaborators' (and perhaps prosecute them, as it may difficult to pardon 'everyone'). To know what happened to perhaps help prevent it happening again in the future.