Two years ago I was at the checkin for HKG-SYD on CX and as I had a new passport my Australian visitor visa had 'expired'. Check-in agent asked me to go to their service desk where staff sorted it out for me (i.e. applied for a new visa) and this took about 10 minutes. I had to pay a service fee of approx HKD400. I have an EU passport.
I had a similar situation 8 years ago in Denpasar. I was ignorant about the whole e-visa/advanced travel information thing for Australia at the time and wanted to check in for a Jetstar flight to Sydney without having this. The Indonesian ground staff could not check me in for this reason. A supervisor was called who had a laptop connected and arranged it on the spot. Not even a service fee asked. In indeed something like 10-15 minutes. I am an EU (Schengen) citizen. Worked a bit like US ESTA at the time with almost instant confirmation. Excellent service of the ground staff. OP seems fine to me as far as the flight concerns, and I guess providing the e-visa information twice with different passport is something you can explain if an issue when entering Australia at all (PS see now that OP indeed had no issues boarding the flight and entering Australia).
Last edited by atflyer; Sep 7, 2019 at 10:10 pm