It's pretty clear from this story that Berger had his hands on the original versions of various interim drafts of the Clarke memo, and the interim drafts may have contained some damaging points that were 'deleted' from the offical report.
From the Sun story:
"Accounts differed on how many documents were missing. One source said five or six early versions of the Clarke critique - ranging from 20 to 30 pages each - were missing.
Berger had previously aroused suspicions, one source said, because several reports he had looked at were missing. The staff called Bruce Lindsey, former deputy counsel to President Bill Clinton who was a Clinton liaison to the archives, to offer a chance to clear up the issue and retrieve the records, the source said. Lindsey could not be reached for comment.
The source said the records Berger returned through Lindsey were not the same records the staff had suspected were missing, which suggested that more records were missing than the staff had realized. "That's when they started coding the documents," the source said.
When Berger returned for his next visit, the staff watched him as he appeared to put papers in his pocket, the source said. An archives spokeswoman declined to comment."