Yours is the first time that I have seen a comment that the FI installation was extensively re-engineered - not that this would necessarily meet all of the relevant standards, and carrying out a safety analysis is little use if its results were not to be implemented - were they?
I'm only going by what others who appear to have the credentials to know have reported - I have no direct knowledge of Nimrod AAR. I do not think they are making it up as their testimony, to me, is entirely convincing for a number of reasons that make it clear they are who they claim to be.
As I've said earlier, adherence to standards is no guarantee of safety, and it should be remembered that safety analysis typically occurs in parallel to design activities, in such a way that safety drivers and features will be an integral part of the design. Failure modes would be considered during the design and mitigated. My experience is that our industry are responsible and diligent in this respect. Safety analysis in this correct sense therefore is not a 'bolt on' activity afterwards when expensive to change design decisions have been taken. Furthermore this does not preclude 3rd party assessment either, both in terms of an Independant Safety Assessor (ISA - or its 1970/80/90s 'equivalent') being involved during design reviews, and also of course having your boscombe down types reviewing design reviews as well. I have no direct knowledge but feel fairly safe to assume this kind of safety analysis would have occured during any AAR re-engineering.
All of this aside having seen how the Chinook BOI was "manipulated" (which I will happily justify in a PM if you wish) I am, like everyone else, very suspicious of the reasons for the continuing delays!
Would like to hear more of your views on this, though to be honest my views on Mull/Chinook are, and I'm afraid some may not like this, is a 99.99% probability that the crew flew a Chinook that was operating normally to all intents and purposes into the Mull. There is much debate on the remote technicality that it could be something else, but when you look at the big picture it is extremely unlikely. I must stress that this is not to say that I agree with the negligence verdict for a number of reasons, but this is a different issue to the airworthiness of the aircraft in question and the bearing this had on the crash (i.e. to all intents and purposes from the balance of evidence available, absolutely none).