The "Directorate of Flight Safety" is actually the "Inspectorate of Flight Safety" or IFS. Sadly the single service RAF IFS at RAF Bentley Priory became the joint service Defence Aviation Safety Centre (DASC) that then became DARS (can't remember what that stood for) at RAF Northolt before being broken up into the Military Aviation Authority (MAA) accross many locations. All this took place over the space of 10 years and so the NART report from 1998 could quite easily be lost. Don't forget that 10 years ago intranet sites were just coming in and I believe that the 1998 NART report would either be paper-only or even worse on CD ROM. Certainly the Sentry Airworthiness Review of the same period was on CD ROM only with the odd paper copy.
So where could it be? Filed away with lots of paper files kept at one of the file repositories, languishing in a desk somewhere at Kinloss or the back of a filing cabinet in Flight Safety organisation, or just plain lost. Don't forget that paperwork can be destroyed if no longer required after a certain amount of years gathering dust (and rightly so, because otherwise the RAF would be drowning in paperwork following its short 93 year history).
The fact that the RAF can't find a copy doesn't surprise me. A copy might turn up, but don't hold your breath. I don't believe there is any conspiracy theory at play here or with Chinook.
LJ