[TheForceOfOne]

I am only guessing at best

We all are, speculation based on whatever knowledge we have or think we have. lol

We need to know what the procedures were for dealing with electronic data, and electronic data in a highly classified area which little old me will never know. I would think the red tape you would have to go through in government alone would hold up erasing that information for a couple years.

[Marine_Uncle]

"I am only guessing at best."

Most if not all are making guesses. And if someone here works for the DIA chances are they would not say much if anything.
I suspect each agency has it's own set of rules regarding electronic publishing, data backup, etc.. As mentioned elsewhere, it could simply be possible, if the project AD was working on indeed did get closed down. Pertenent documents in the form of reports would have been printed out, distributed to those designated to keep them, then the hard disk data erased. But I still maintain, depending on the nature of a given project, one does not neccessarily erase hard disks (surface destruction of the bytes forcing for instance every byte location on every track, sector, and cylinder of a disk to read a NULL character, or a zero or all ONES, etc.. There are mainframes that continue to hold vital information accumulated for years, that are vital to defense/security. It is to easy to just say a project is shutdown. Sometimes projects/operations are dormate, ready to start up on a moments notice if required. I am sure we shall never gain the details nor should we of what type of operation AD was involved in as far as what type of tools it used. What though is hard for me to buy is that Schaffer would have let anyone know other then a really well known friend within the DoD ranks what he was storing and where.
The only alternative, is it is a inside DoD job, where someone in the Pentagon with high enough authority was able to get access to the 15 boxes of materials that are supposedly held in a secure location, within the Pentagon,
and pilfered the stuff, without being noticed, hard to do, but perhaps possible if people where paid of to cooperate.
But somehow I don't believe that would have happened.
Lets remember Sandy the Burgler was viewed by video for a number of days, they in essence set up a sting. They let him sign stuff out, sneak it out then not return it and sign it back in. Surely secure areas in the Pentagon and other military installations must have adequate security monitors.

Then again, like you say. We are all guessing.