C240
You used the argument about time in service, in the same way MoD justify all their decisions with "There haven't been any more Chinook accidents, so it must have been safe in 1994". If that is not what you meant, it is better to avoid confusion and look at the situation as it was at the time. That is, the Chief Engineer and ACAS were sitting on a report telling them at least 5 crashes had been caused by airworthiness failings. THAT is the important fact and what ACAS had to consider in Nov 1993. These officers need to be asked what they did about it. (CDP already answered that for the major criticism, in 1999 - nothing).
Like I said, there were two upgrades. If you say they were never embodied, that is a slightly different thing and I of course accept your word. However, what later evidence demonstrated was that the major (FADEC) failings perceived at the time by Boscombe and RAF pilots were partly resolved as they came to understand their nature. Such failures during testing demand you stop and try to work them out. If you cannot explain them, then you cannot prepare, for example, AMs and FRCs that are fit for purpose; or determine what limitations to set out in the RTS. That is, the technical maturity, which includes understanding, is insufficient. That alone prevents a Certificate of Design being issued because you cannot declare the product compliant with the spec when it cannot be verified; but the project manager may decide to sign an Interim CoD to allow flight testing to proceed.
Anyone familiar with this process can see that, on 2nd June 1994, the Chinook HC Mk2 did not meet the mandated maturity levels (based on recommendations from the Chief Scientific Advisor and endorsed by SoS). On that day, the HC Mk2 was not airworthy. The programme status was that of an immature design in early testing, with Safety Critical Software not yet validated or verified, and no Comms or Nav systems with Full or even Limited clearance. (Largely because representative testing could only commence once the FADEC software issue had been resolved).
But, it can be seen that with no further modifications it may have become airworthy, as understanding matured. From papers I've read, this declaration was made in January 1996 with Issue 6 of the RTS. I hope that answers your question.