Hi Andy,
I was just helping out someone on our forums regarding a similar issue. You can only move the contour to a new object if that object is on the same plane as the first one you tracked. If that's not the case, you are better off creating a new layer for the new object. Then export each layer separately and combine the results in AE.
The hard part is getting the surface from each layer to align, but depending on the magnitude of the stabilisation you're trying to achieve, this might not be necessary. If there are some features in shot the whole time, you can align the surface of each layer to them by eye. If not, I would recommend using the Align Surface button on the first frame of each layer, then lining things up in AE.
I don't know the details of how to merge the data in AE, but I'm sure it's possible using nulls, parenting and expressions. Maybe someone on here who's an AE expert can help out?
Best regards,
J-P
John-Paul Smith | CEO | Imagineer Systems
www.imagineersystems.com