Support the IModelXmlConverter interface in your Module and implement the ConvertXml method, to make the required changes in the model differences. This method is invoked for each node customized in differences and takes the ConvertXmlParameters object as a parameter. This object provides you with access to the node stored in differences. With this method, you can handle, for instance, changing the type of a certain node.
Refer to the Convert Application Model Differences topic to see the example.