Sorry for getting back to you late, for some reason I haven't been aware of this update.
Anyway, back to your question.
When you duplicate the data frame, did you check 'Include Viz'?
To export EDF with Viz, you want to select 'Export Chart as EDF', though this would export only one chart that is currently selected.
In order to point to a new data file, you can simply click on the green box or 'Edit' button at the Source step. This will open the data import dialog where you can point to the new data file.