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If transformations that input or output UML models are to be generated then the UML metamodel must be added as a root input and/or output of the mapping specification. The addition of a UML profile to the mapping specification does not automatically add the UML metamodel too. The UML metamodel can be added via the Add Model buttons available in the Model-to-Model Transformation Mapping Wizards and Editor.
If a user switches feature filtering from "Basic" to either "Intermediate" or "Advanced" mode, creates mappings, and then switches back to "Basic" filter mode then some of the mapping endpoints might not be visible any longer and consequently the mapping connectors may seem to now have ends that don't connect to anything. This is only a presentation issue; it does not affect the mappings or the transformation source code generated from those mappings. The presentation can be corrected by switching back to the filter mode that was in effect when the mappings were created.
When a mapping file no longer contains any mappings that specify elements from some particular model as mapping inputs (outputs) then that model is "dropped" from the mapping file. The check for unused models is made whenever a mapping input or output is deleted. Separate lists are maintained in the mapping file for inputs and outputs. Once a model has been "dropped" then it must be re-added (via the Add Model buttons in the Mapping Editor) before elements from that model can again be specified as mapping inputs (outputs).