It sounds blindingly obvious, why hasn’t anyone asked for a copy of the 29(F) Sqn F540 Ops Record Book (ORB) and also the QRA Duty Force Commander (DFC) log for the date of the alleged event? Both are likely to have been preserved by the Air Historical Branch (AHB) and even if secret then this is coming up for 50 years ago and should be releasable in redacted form. Also a FOI request on the numbers of Red Top missiles fired may also see an anomaly if a missile really was fired - which I really doubt in this event, but Rick may have got confused if there was a QRA missile practice firing in Aberporth around the same time. So a search of the STCAAME logs from RAF Valley or Llanbedr may also put another piece of the jigsaw together.
There are so many things “fishy” about the quality of the BBC article:
There is an account of that Wattisham operation in a 2011 book called The Lightning Boys. In it, former RAF pilot Rick Groombridge details how an American exchange pilot took over his aircraft at Wattisham to take part in the Meyer mission and was rumoured to have returned to base minus a missile. Groombridge declined to be interviewed but stands by his story. Nash, however, is adamant that both planes returned to base with all four missiles intact - he should know, he explains, as he was the chief armourer and was responsible for inspecting the weapons and removing the firing plugs.
A few weeks after the incident, Nash was sent on a course where he met a fellow armourer from RAF Chivenor in Devon, who told him that at least one Hawker Hunter was scrambled from his base. Allegedly, the Hunter pilot had returned to Chivenor minus missiles and was met by the RAF police and taken away for a secret debrief along with his plane's camera gun. Nash says he keeps an open mind about the accuracy of the story but observes that Chivenor, being about 150 miles from where Meyer's Hercules went down in the Channel, was about 35 minutes flying time away for a Hunter.
The Hunter never had missiles, let alone the ones at Chivenor, that were a part of Phase 2 Flying Training for tactical weapons conversion. The ‘rumour’ at Wattisham is probably just that, and sells books, so I am not surprised that Rick G+10 sticks to the story of the rumour.