Load from file Equivalence links in MPMLink

We are in the process of rolling out MPMLink and want to load all of our bom's from our erp system into different views.  The issue I am having is when I load the new view and make the equivalence link the bom from the design view is duplicated to the manufacturing view.  When you do this process in the BOM transformer the UI has an option to "Do not Duplicate".  Does anyone know of a way to stop this from happening when using load from file?