Ok, so here's a final update on the saga:
In November I got the reply back from A3 and submitted this to SA. This obviously was a very painful conversation with a call centre agent who had no idea how to deal with this (granted it's a pretty exotic problem). She transferred my query to a very competent supervisor.
She immediately understood the problem, but also said that she doens't think they have any way to deal with this as a standard process, but that she would chase it up with the "Systems" department. It seems like they spent November trying to sort it out.
In early December I got a reply from SA and A3 saying they have resolved the issue and that my miles would be credited.
Checked two days later and all the missing miles are (in the correct classes) displaying on the A3 side now.
All's well that ends well.