Whenever important documents like these are destroyed, it must be because the penalty for destruction of documents is much less than the penalty for what the incriminating information that the documents would have exposed. I recall this happening during the Clinton administration, especially in the Chinese funny money hearings
I think it would be reasonable to remove the presumption of innocence from government agents who destroy records in violation of law.
Similarly, if someone is convicted based on evidence claimed to exist, and then the evidence is willfully destroyed, the destroyer should get the same penalty as the guilty party, and, depending on circumstances, perhaps the convict should be set free.