The NPPL and UK PPL are totally different licences.
Without a JAA Class 2 medical, the pilot's UK PPL was invalid. If he then flew a SEP or SSEA aeroplane without a valid medical, he did so illegally.
The Examiner who signed the Sep 2005 validation should have checked that the pilot held a valid JAA medical. If he changed to a NPPL in Sep 2004, he would have had difficulty in completing 12 hr PIC and a 1 hr training flight in the last 12 months of a Rating expiring in Sep 2005.
As regards the NPPL, he could quite simply have arranged for both SSEA and SLMG Class Ratings to be included in his NPPL at the time of issue. Why did he not do so? He was very poorly advised.
If he wishes to fly SSEA aerolanes, he will now need to complete the relevant training and apply for a SSEA Class Rating to be included in his NPPL. Any illegal SEP Class flying will be readily apparent in his logbook; however, the CAA do recognise that many pilots have misunderstood the NPPL requirements (hence the forthcoming ANO change), so it is highly unlikely that he will find himself in trouble.
Without a JAA Class 2 medical, he cannot fly on his UK PPL; without a SSEA Class Rating, he cannot fly anything except SLMGs on his NPPL.