Funny, I just went over to the NYT site and their article actually says Berger returned all the documents. But AP and Reuters quote him as saying he discarded some.
I had trouble with this at first, too. As I've scanned through these articles, I think the answer to you question is:
1. Burgler claims (and the press has faithfully reported) that all the 'relevant' Clinton-era documents were sent to the 9/11 commission. That all he took 'inadvertantly' were copies, so 'naturally,' the 9/11 commission was not deprived of the originals.
2. In his account (and what the press has reported for him) this means that 'all' the documents were sent to the 9/11 commission.
3. What the press is having trouble 'decyfering' is that what he stole from the room were draft reports of what became the actual report which was sent to the 9/11 commission.
4. The press is just reporting his claim and has not yet had time to ask him, "Well, if you 'inadvertantly' took draft copies, of which no originals may be available, and then 'mistakenly' discarded them when you washed your socks, them how can you claim that 'all' the relevant documents were delivered to the 9/11 commission?"
In other words, the reporting is focusing on 2 things -- what was sent to the 9/11 commission (everything, Burgler claims) and what he returned to the archives after he was caught.
The question now becomes, what was in the draft reports that made him take them. I'm betting PC stuff, and as usual, what was in the draft reports will not be as damaging now as the cover-up.