John,
I've searched the St John Ambulance Brigade rolls, both page by page and digitally and the only Prescott I kind find is 1300 Pte. J. Prescott. He was with the Rhodesian Field Force Hospital and both rolls (first done by hand, second neatly typed up) show him as getting QSA with Cape Colony and Transvaal clasps. No notes appear under remarks linking this man with the RAMC roll or noting a death. If you could ask the Curator at St Johns Ambulance Brigade if he could give you the service number of the H Prescott they have on their records.
What are the details on the rim of the St John Ambulance Brigade Medal you have? We may be able to clear this up from those if his number is 1300.
A possible explanation here might be that because the Prescott on the SJAB rolls was not linked to the H Prescott in the RAMC. If this is what happened then there may well have been a double issue of the QSA to the same man but from different units. Usually when a medal is returned it is noted on the roll. No returns appear to be noted for either the SJAB man or the RAMC man.
I guess when the RAMC QSA arrived it was taken as the deceased H Prescott's medal and that was it. Then the SJAB medal arrived and with that it would have appeared that all medals were accounted for. Who knows what happened to the SJAB QSA if there ever was one.
If Prescott did earn a Cape Colony clasp while with the SJAB [it certainly looks very likely he did] then with the failure to match his service in the two different units resulted in the QSA from the RAMC not including a CC clasp. If Prescott did earn the CC clasp with the SAJB then you could always purchase an original CC clasp and keep it with the medal. If you PM me your e-mail address I'll send you copies of the documents I have.
Cheers,
Mark