I asked the agent for both AS and CX PNRs. The reservation was generated just never had confirmed seats. Hence on CX site using the CX PNR could pull up the "phantom" reservation with both segments showing Waitlisted.

Always ask the agent the PNRs AND ticket numbers. In the above case the agent only had PNRs because tickets should not and could not be issued due to phantom seats but the inexperienced agent had no clue. She told me there were tickets and I would receive the email within 24 hours, but she actually confused the PNRs with tickets. LOL.

I believe AS has done a lot of clean up on the glitches - the earlier reservation that agent replaced LAX-HKG with BOS-HKG-NRT, is showing up with details. I booked a NRT-HKG-BOS online myself when I decided to check availability on BA site since one direction saw a lot of new availability, the other direction may follow suit. Sure enough there are availability scattering in the first 2 weeks of Oct with at least 2 days have 4 seats available. NRT-HKG has TONS of availability in both Sept and Oct.

Also what the phone agent said about 7 days stopover restriction at HKG might not be true because late at night I was able to book with 12 days stopover on the return NRT-HKG-BOS online.

The booking was confirmed fairly quickly, quicker than the LAX-HKG I did earlier today. Then A SLEW of emails coming from AS, including the LAX-HKG already cancelled by the agent. One email is truly screwy with the $ charge breakdowns. It showed $5.60 tax and $25 partner booking fee per person, and a total of $61.20 charged to my AMEX - But the AMEX pending charges showed exactly as what the phone agent told me - the $12.50 x 2, the $5.60 x 2, from the previous LAX-HKG, and the balance of the taxes owed at $86 (actually is $42.90x2 = $85.80 but AMEX pending amount seems to round it up). So will need to monitor the actual $ posted to the card.

We really need at least 2 weeks time in Hong Kong to take care some stuff which have been long overdue. Even 14 days are fully available, it might be barely enough because it takes time to get things processed with the government depts. Therefore we would need to stopover at Hong Kong on both directions anyway. The time spent at the "final" destination would provide the needed time to get things processed. Now we have first 7 days in Hong Kong, 7 days in Japan, and 12 days in Hong Kong again. It should be enough time to get things processed. I would still prefer to head to Australia instead of Japan mainly because for an extra 10K miles that is a much better value. Since we have to go to Hong Kong we might as well go further south as well. Though for the time being I am glad to have taken care of TPAC on both directions.