As per the commercial policy for the changes:
https://www.qantas.com.au/agents/dyn/qf/info/201210/1004
For Australia – London v.v. customers -
- Re-route/Re-book travel between Australia and London via an Australian Gateway (Sydney, Melbourne, Brisbane, Perth and Adelaide) on:
- Qantas marketed and operated flights to/from London; or
- Qantas marketed flights operated by British Airways via Singapore/Bangkok; or
- Qantas marketed and operated flights to/from Frankfurt connecting to Qantas marketed flights operated by British Airways between Frankfurt and London; or
- Qantas marketed and operated flights to/from Frankfurt connecting to British Airways marketed and operated services between Frankfurt and London
While the separate PNR may cause an issue, its should be made clear that due to availability issues it was the only way you could book travel to LHR at the time.