DozyWannabe: I will try and answer your questions and points in the order you have made them..
I don't know how long the transponder light was on for, and neither do you, so we are both speculating.
You say that "As far as Collins is aware, the radar controller will not approve a let-down until they are positively identified".
You are completely wrong in this assumption, the radar controller cleared Collins for a VMC descent. In doing so he handed complete responsibilty for cloud avoidance and terrain clearance to the crew, without any suggestion of radar identification or flight following.
I have issued many hundreds, maybe thousands, of VMC descent clearances to aircraft on IFR flight plans and it was never understood by any commercial pilot to mean anything other what I have stated above.
In that knowledge, Collins was not entitled to take the controller's assent to the let-down as confirmation that everything is safe for him to do so, nor do I believe he would have assumed it to be so.
You mention again your belief that a brief part of the radar trace was deliberately destroyed.
To do so you are making another assumption, neither you nor I know for certain how that part of the tape came to be erased.
Do you know what playback equipment was used ? do you know if the tape was frozen post accident knowledge, and if so, what safeguards were there to preserve it's integrity ? do you know who was authorised to make any playback, pre or post accident ? do you know if accidential erasure was possible on the type of playback equipment used ?
In reply to ampan's point you appear to making the mistake of believing that because the aircraft was just within the radar maximum range it would have shown up.
Surveillance radar does not necessarily work like that, there can variations, holes, and gaps in coverage for a variety of reasons. Particularly as the radar at McMurdo was, as I understand it, by no means new.
When I was working I could have shown you several instances where an aircraft well within the range limit of coverage, would be on one track at a specific range painting loud and clear, but if it had been on another track only 8-10 miles away at exactly the same range it would not show at all, not a glimmer of a paint
This was, I will add, using a radar of similar vintage but longer range capabilty to that I understand was in use at McMurdo.
Secondly, in your reply to ampan you say "the transponder was coding at 15:21 - 26 miles east of where he was expecting it (which means that they probably did show up) - why? It's not like he was distracted by heavy traffic..."
It may or may not have shown on the radar, regardless of whether it did or did not show, by then Collins was accepted a VMC descent and, as I have already explained, had accepted complete responsibilty for his flight safety.
Knowing this, the controller might well have looked away from the scope to talk to a colleague, or perhaps perform some other admin task.