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Per Michelle Malkin:

Archives officials have said previously that Berger had copies only, and that no original documents were lost. It remains unclear whether Berger knew that, or why he destroyed three versions of a document but left two other versions intact. Officials have said the five versions were largely similar, but contained slight variations as the after-action report moved around different agencies of the executive branch.

If one carefully followed last summer's coverage, it became apparent that each of the 5 versions [taken by Berger] bore unique handwritten notes or markings made by its recipient. That means each copy became an "original" document, i.e. containing information not depicted on the others.

They were not exact copies; each memo started off as a copy of an original draft by Richard Clarke, but the memos had handwritten notes from each recipient as comments, requests for revision, and suggestions for possible action. Each document was unique, and their destruction by Mr. Scissors means that we will never know what some did with Clarke's information. All we know is that it must have reflected badly on Berger, Clinton, or both. Otherwise, why would Berger destroy them?

Source

So...it depends on how you define the word "copies".

"Each document was unique, and their destruction by Mr. Scissors means that we will never know what some did with Clarke's information. All we know is that it must have reflected badly on Berger, Clinton, or both. Otherwise, why would Berger destroy them?"

Exactly - this strikes me as the only explanation that could account for why Sandy Burglar was willing to commit crimes and risk serious jail time. Mere 'carelessness' is no explanation at all. fwiw, I have family members who hold or have held very high security clearances, including one (now retired) who worked under one of the top few military officials in the country (pre-Clinton years). They all find the explanations of Burglar and Clinton of how this all transpired to be so preposterous that they laughed uncontrollably (and then were extremely angry) when the Burglar-Clinton explanations first became public. They tell me that even far less sensitive documents are handled with so much more care (except by Clintonistas, evidently), that even misplacing one WITHIN a secure office (never mind removing it) can be a career-ending move. No, whatever Sandy Burglar was up to, he was desperate to make sure certain documents, probably including hand-written comments by top Clintonistas, never made it to the 9/11 O-mission. Even if such documents are termed 'copies' and there is still an 'original' somewhere in the NA, it looks like Burglar made sure that hand-written notes were deep-sixed.... and the 1998 after-action report on the cruise missile attacks never made it to the 9/11 O-mission in any form.