Not exactly the same but similar. I had to split the original DSC booking into two (the second passenger wasn't travelling) and to cancel one ticket. The agent cancelled the old PNR, and created a new PNR for mine, although I specifically asked for the old PNR to retain. I called the FF team and they listened to the tape (or maybe just looked into what happened) and confirmed that my new PNR would still be eligible but they would have to do a manual processing (they made an internal note on my account or PNR, not sure).
Upon completion of travel, as expected, DSC didn't post so I called and they investigated, but had to wait until the obligatory 12 weeks waiting period. The FF team supervisor was really through, and assured me that she would put a reminder in her calendar to check my account after that period lapses. Shortly after 12 weeks since the flight the bonus SCs were credited, so despite the sales team initial stuff up I am pretty happy with how QF handled it.
I suggest try calling the FF team and seek to speak to a supervisor.