This fairly difficult... I'm not sure if cpanel's backup facility provides for this, but as long as you are taking the entire directory structure of the account in question, you'll grab all of the edited files/templates that go along with their interchange cart. The configuration for each cart as far as the interchange daemon is concerned is within /usr/local/cpanel/3rdparty/interchange (interchange.cfg).... somebody correct me if I'm wrong.
That's the only file that actually is vitally important to interchange running for each particular cart. Otherwise all of the data is stored within the user's account space. It's very tricky though, if you move a cart physically, make sure you make the necessary changes to the interchange master config file manually or there will be major problems down the road.
Anyone know if the account move feature does interchange carts very well or not at all?
Peace.