I have two versions of my model Model001.xcdatamodel and Model002.xcdatamodel. These two are in the Model.xcdatamodeld bundle. I also have
Model001.xcdatamodel
Model002.xcdatamodel
Model.xcdatamodeld
OK, solved the problem by removing all core data files from Xcode, reading them and setting the source and destination of the mapping model again.
Damn you Xcode!