I have a related problem. My mtl file recognizes my two metamodels but after running the file I do not get the correct result because it seems that the generator can only access the instantiation of my first metamodel and not the instantiation of my second metamodel.
Put differently: Is it possible two add 2 models as input files which contain references to each other.
If you want to use multiple models in your generator, you should start with one of the models and then navigate to elements of the second one in the generator. If the second one is not loaded, you can use the code in the comment in the method "doGenerate" (//org.eclipse.emf.ecore.util.EcoreUtil.resolveAll(model)).