What exactly was your source for this particular information?
A book but since you all have so much affinity for the Internet I found this which says the same thing as the book essentially:
Court stenographers recorded the proceedings in short hand known as computer aided transcription notes. These were filed separately from the case file and
not kept permanently. However,
if the defendant lodged an appeal within five years of the conviction then long hand notes were recreated from the original computer aided transcription notes for the appeal and
may be found on the criminal appeal case file http://www.nationalarchives.gov.uk/help-with-your-research/research-guides/criminal-courts-england-wales-from-1972/#6-transcriptsThis notes:
1) that the CAT notes were destroyed after 5 years
2) that if an appeal was filed within 5 years then prior to destroying the CAT notes they would have been transcribed into a full transcript.
3) The full transcripts MAY have been retained in the appeal file but for a variety of reasons they might not have been kept in the appeal file and may not have survived.
If they were not retained in the appeal file then one is sh$t out of luck. Obviously the transcript of his testimony in chief was not found in the appeal file or the 2002 COA panel would have found it. They noted it was missing from the file.