Ok. I am on a project for a client. I have inadvertently recreated the scenario, and I have pictures. Fig 1 shows a piano region highlighted, the event window showing the highlighted 6 bar region, and the undo window. Fig 2 shows the highlighted overdub 3 bar region on top, and overlapped and the edit window showing the same highlighted region. Now I decided to quantize the notes in the overdub, overlapped 3 bar region and the underlying 6 bar region disappears. Poof! Fig 3 shows the result. You can the undo window shows the action of the quantize and no deleted sequence and the event window showing one 3 bar sequence and the other 6 bar sequence is magically gone! Ta-dah!
Am I doing something wrong, or is this a bug. By the way I've been using Logic professionally since OJ was on trial.