Alec,
I believe where some of the confusion comes in is that in actual live play most of us hit the ending button before the end of the last measure of the song. The keyboard is smart enough to not actually start the ending sequence until the next measure.
As I see it, this is where the "delete" problem arises. The Ending Command (*) is placed in the control track 6 at the time the button is hit - in this case, in the measure before where you hear the ending. However, the sequencer records the ending APC data (track 5) in the measure where the ending actually is playing.
This means that when listening to a sequence, lets say that the ending starts in measure 48, you must erase the ending command (*) in measure 47 because that's where it is. Track 5 with the recorded APC ending would be in measure 48 so that's where track 5 must be deleted.
I have had the best luck just using Measure Delete>All starting with the measure just before the ending. This leaves the end of the song intact and has deleted the ending every time.
Regards,
Walt

[This message has been edited by Walt Meyer (edited 09-09-2003).]