Recently I took my self off to Chester DVLA branch, having read on the MCN forums somewhere that you can get a certificate of some sort confirming the entitlements on your drivers licence before sending off for any kind of update.
Iot my ticket number, waited for about 20 minutes, came to my turn and so approached the counter and enquired about said slip/certificate.
"No such thing" said the rather helpful lady. "It's something that was a problem for a very small section of lisence holders, incuding the boss being hauled on Watchdog... twice. It was pretty much blown out of all proportion."
However, she went on to say that though it was highly unlikely now that my bike entitlement would be lost, she did recommend "photocopying both parts", as they "would accept this as proof if there were to be a problem."
It seems the only other way to minimise this risk is to go with the advice in MCN this last few weeks and send in the SAE and a covering letter asking for my old photo card back, missing it's corner.