Dangermouse
I would add that if MoD chooses to ignore Boscombe’s advice, any Safety Management System (and certainly MoD’s own) requires reasoned explanation to be logged.
Not only that, but something like the FADEC issue would immediately be logged as a risk (if it wasn’t already), and the same rules require a full record to be retained even if the risk is fully mitigated or deemed erroneous.
It cannot be acceptable for any MoD officer to say that a Boscombe report stating there is a safety risk can be ignored. It must be investigated. Equally, it cannot be acceptable for a contract to be paid off, the aircraft offered to the RTSA and the RTS signed, in the full knowledge that it is physically or functionally unsafe. But that is precisely what the Chinook 2 Star in MoD(PE)/DPA ruled.
It is rulings like this which have prompted IPTs to adopt a too literal interpretation of “Boscombe only give advice, we don’t have to take it”. They don’t have to accept it, but they do have to investigate and state why they don’t; and record the reasoning.