The question of interchangeability (or otherwise) is managed under PDS. The top level drawings will have a series of "call ups". The Requirements Manager (or whatever he's called now) is required to be aware of the major issues - a typical example is differences in dimensions/tolerances between production runs and he has to make sure this is flagged in any proposed contract or modification submission. After MoD stopped doing this in June 1993 enormous numbers of mod sets were scrapped annually; made to fit one batch, and didn't fit the rest. And it was one of the howlers on Nimrod as the mainplanes were hand built, but RAF engineers were ignored. Nothing new I'm afraid.
I tend to agree with ACW342. Long experience tells me destruction of MoD-held records was quite deliberate. But they almost certainly exist elsewhere.