I think the reason is in Visual_ID properties changed in your modified gmfgen
model. Currently you can re-initialize new diagram using the model file.
For future if you want to use the same Visual_ID values for the same elements
of gmfgen model on next gmfmap->gmfgen transformation â take a look on org.eclipse.gmf/plugins/org.eclipse.gmf.bridge.trace
plugin (present in CVS only) you should take it, compile and make running
in an eclipse instance performing the transformation.