I can tell you my recent experience. I, too, had a flight itinerary disappear from the web site. When I called to inquire, it turns out the the new flight times resulted in an illegal connection. The system writes these records to a file to be manually worked. I just happened to discover it before a Delta human being got to it. In my case, the trip couldn't be systematically re-worked because my departure time was going to have to drastically change.
[This message has been edited by RRWhite (edited 10-10-2000).]