I was able to change my AFKL number to my Alitalia number using the Garuda website on a Flying Blue redemption booking. The status did update from Elite to Elite Plus on MMB, however it still insisted on printing the AFKL number when I did OLCI.
Amazingly the Menzies agent at Arlanda managed to reprint my boarding passes with the Alitalia status. So it can be done!