Perhaps in one of the deleted files Avid is storing the tracking data pointers but not the tracking data itself. In my experience the tracking data will stick with the effect but gets off when people start trimming the effect or just taking a part of the effect. If the effect has already been rendered the move stays in place but when it becomes unrendered it will no longer track properly. Redoing the track on the altered duration effect will usually get the tracking to work properly. In cases where people have tracked a dot shot handheld for approximately 30 seconds and then taken that effect and applied it to a much shorter shot it seems like the tracking data still causes a handheld movement to the image even though the shot is much shorter in duration. This behavior seem similar to when moving picture moves are render and then someone trims them. As long as the effect is never unrendered they don't see any problem in offline but when in online the unrendered moving picture is missing the original start and or end keyframes that were trimmed out. I wonder if there is something similar under the hood here. It is interesting that deleting those files would make the tracking data re align itself properly. Have you tried redoing the track without without deleting those files or are you redoing the track after trashing those files? Very interesting interaction.
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