In your new Interface file you want to put the relationships to the Data file (the original file). Yes so the interface file, that you will later put on your mobile device, is where you add the table occurances that are to the data file. It will not effect the relationships in the data file. Although in the data file a minimal amount of TO's are needed. Most of the working TO's are in the interface file.
I second Ben's point: your baisc relationships need to be defined in the interface file's relationship graph using TOs based on the tables in the data file. Minimize the relationships in the data-storage file, leaving the basic TO for each table in the data file on the graph, even if not related in any way. Let the interface file carry the relationship load as much as possible.
This will also minimize the need to fiddle with the data-storage file's graph down the road, allowing you to update the interface file independently -- the real benefit of the Separation Model.