Yes, I have visited a few airport and city offices over the last few weeks, but the issue isn't fully resolved yet. The BLR airport ticketing office did recognize the problem and said it would be an issue; but told me to go to the city office to get it fixed since it's an award fare bucket. The Bangalore city office just checked the ticket number, confirmed everything seemed ok, printed a copy of the e-ticket receipt, and said the missing reservation wasn't a problem.

The staff at the Mumbai city office at Nariman Point were the most competent, they quickly understood the issue and reviewed all the e-ticket details and confirmed that there was a mismatch that needed to be resolved. It seems that now there is no longer any PNR record in the new Air India Amadeus system for those flights after migration, since the cancelled PNR from the old system wasn't transferred. They made some calls to the IT / migration departments and said they needed to send the details to those departments to resolve, and it would probably take a week. It's been about 10 days now, I have called to follow up, and they've said they're still working on it. I'm not sure if they will eventually be able to fix it, or if it will still be up to the check-in staff to resolve it.