Ancdotally, it doesn't seem like any automated process will solve this, because i think at least 50% of the problem is harried agents. I had a single PNR split into 3 separate PNRs by the integration. 1 with my name and correct seat, but for only 1 leg (the former CO leg) of the trip. A second for my wife, with the same problem. And a third with all correct legs showing, and both passengers, but the "needs reissued" problem.

When i called to resolve this, since our flight is tomorrow, it took them about 30 mins to fix. They reissued the "correct" PNR and cancelled the two partial PNRs... But this dumped our seats, and by the time everything was fully fixed, our seats were gone, and only middles remained on that flight. Nothing they could do.

I believe that the agents COULD have captured/retained our seats during that transaction, but it wasn't a priority since they've probably spent all day reissuing tix. Given how one of my other itins got cuisinarted as well, i suspect that seat assignments followed the "old" PNRs, and if you had a mixed-metal itin affected by the reissue problem, your seats were dumped when that partial PNR was.

I'm more inclined to blame human carelessness here than putting all the vitriol on IT...