So an update on this: as per my previous post they fixed the loyalty bonus SC tally on the website to include SC's earned from Classic Flight Rewards so visually everything appears to be in order.
However, it seems they haven't adjusted the automation that actually awards the loyalty bonus to follow this logic as well. With SC's from Classic Flight Rewards, I earned over 500 SC's towards my loyalty bonus which was reflected in the loyalty bonus tally on the Qantas website. However the loyalty bonus never came through. Speaking to the FFSC, they've advised that the system has only included SC's from revenue QF/JQ flights and the total they are giving me on the phone is my total without Classic Flight Reward SC's.
Going around in circles with the FFSC trying to get this fixed now and they are looking into it but it is taking weeks. Has anyone else had this issue and did you manage to get it resolved? If you're a Points Club member it may be worth checking to see if you're owed a loyalty bonus!