I've seen the same thing on a few CT sites but never with any source for it. I have a few problems believing it though. Firstly, because DoD audits are not really done at the pentagon. DoD has auditors all over the country and they generally go "on-site" (to wherever a given companies headquarters is) to perform the audits. Once completed, all audit reports are filed at the regional DoD office, on computer and sent electronically to the pentagon. Now, I certainly can believe that people at the pentagon were reviewing reports to look for mistakes to find "lost monies" but they would be working on the DoD mainframe, not hard copy originals that if lost had no replacement. It just does not work that way and it has not since way before 9/11. So for this to be true, the DoD mainframe and all disaster recovery back-up would have to have been where the plane hit... I really have a hard time buying that, so much more would have been lost beside accounting files.
I've heard the same about enron in building 7 and have not seen any reliable source for that either. I have a hard time buying it as well and for the same reasons. The source of the enron rumor seem to come from Barry Zwicker in The 9/11 News Special You Never Saw, Global Outlook magazine (Issue 9, Fall/Winter 2005). On page 19, he says "Now this was late 2001. This was at the height of the investigation into Enron, so the majority of Enron's SEC filings were likely destroyed when world trade center 7 came down". It is true that the SEC had offices in building 7 but Mr. Zwicker never explains why he think enron's SEC filings would have been lost (the SEC had lots of other offices) or why there would have been no back ups. Even if it were true, enron would be in possession of originals and more copies could easily be had but of course, I see no reason to believe it is true. I mean... it is not like the investigation of enron stopped.
Source of Barry Zwicker comments:
http://www.greatconspiracy.ca/pdfs/TGC_transcript_GOIssue9.pdf - page 19, bottom right side.
I look at things like this from a tech point of view. I'm a mainframe programmer and have been involved in disaster recovery efforts for about 20 years now. The losses that are being claimed just don't sit right... it's just not how things work.