We are aware of this problem and will schedule fix for it. The only workaround at the moment is to checck-out the class files which you want to modify via the wizard.
Can you consider using the visual DSL designer to model your classes? We recommend using that as it is more feature rich and also integrates with source controlled artifacts.You can use the 'Convert to Domain Model' tool (beta) to convert the reversemapping.config file to a DSL model.
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