As I understand it, they were indeed copies, the originals were still available, BUT NOT TO THE COMMISSION. If the Commission didn't know they were gone, they wouldn't know to ask for replacements.
They were original copies...I'll explain in a minute.
I disagree with the assessment these were taken to brief Kerry up. Here is why. Clarke wrote this after action review to get additional focus on counter terrorism. He wrote the wrote draft, then copies were made, numbered (copy 4 of 10 or whatever) and circulated to relevant parties for comments. Different people marked up different copies with their comments. When all the copies and comments were returned to Clarke, he finalized the review...but he was unsuccessful in getting additional focus on terrorism. Someone's comments shot down his effort, and that someone had to be high up.
I think it very likely that people made comments along the lines of 'politically not worth it' or 'too much political capital' or 'it won't be popular' or 'it won't poll well' The Clinton administration destroyed incriminating documents before they turned over power, but they didn't realize this was incriminating until after 9-11, when they could no longer destroy it. That is why Berger was stealing and destroying documents...it was not Clarke's document itself he was after, it was other people's comments on it. That is why multiple copies were stolen. The Clinton Administration knew the threat and failed to take the necessary measures because they thought it would hurt them politically. They sacrificed 3,000 Americans on the altar of Clinton's legacy. And the documents that proved it had to be destroyed.