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This situation hinges on a fundamentally troubling premise which needs to be challenged for precedent on behalf of a myriad of other cases.
The Bush administration has thrown the label of secret by definition of being a threat to national security to any number of things that would be a hard sell to put realistic logic to. An example would be his military national guard records, embarrassing yes, a threat to national security, no. Financial investigations into malfeasance would have nothing that is a threat to national security even though it's convenient to use that ploy on the grounds that it's military related. It will take an administration with a different outlook than the current one that chooses to flaunt a total disregard for constitutional rights and safeties.
What is such a threat to national security about wiretapping logs? First of all we now know it exists. Secondly the fact it took place has to be acknowledged at the time charges or arrests are made as the result. These actions have to have some legal standing. A person can't be arrested on the grounds wiretaps revealed evidence and then be denied in a lawsuit on the grounds that secret documents are the only proof.
The act of prosecution would demand corroborating evidence that is not secret nor a threat to national security, these documents are part of the record and could be used for any future purpose.
The arbitrary use of the "threat to national security" label will need to have a secret clearance certified board that has the function of reviewing documents in order to determine the validity of the designation. Their ruling would be along the lines of "we see no threat here". The judge presiding over this should have asked if it could be demonstrated that wiretap records could be construed as a national security threat, and if not they would be entered as evidence. There has to be some evidenciary trace of the wiretap program as a necessary check and balance.
By the same logic used by CIA attorneys that it didn't necessarily exist as there are no admissable proofs, the person being charged can't be charged either.
We are going to be aggressively investigating an array of wrongdoing perpetrated by the current administration and there will have to be provisions for using documents that are in no way a threat simply because that is a convenient nullification ploy. This tactic has been repeatedly used to suppress legal issues of all types and has some serious constitutional challenges. The answer may be a board such as a national security threat advisory board that has the final say on that issue.