Thanks for your help, LHR and Dave. Having the two passports seems to cause airlines confusion; the border control staff never bat an eyelid. The only issue with the two passports is that if the Australian one is in the system, they are unable to check me in for the return as it does not contain a U.S. entry permit, so it causes some drama (online and at the check in desk).

If anyone else has tried to switch their details online mid-trip, I'd love to hear whether it worked...

Joe