I have issues with objects that still have an reference instance left over, after the corresponding EReference of the EClass was deleted using .delete(). In this case the reference is still there, but the type in None an makes a .delete() of the object fail. This happened only for EReferences not for EAttributes so far. To fix this, I manually search all instance of the class of the deleted EReference and if hasattr(obj,reference.name) is true, I call delattr(...).