If someone can do this it will be Mendix.
Edit: The modeler is closed so either you need someone to change the flags of all buttons and Only mendix can do this.
The only other option is to see there is an option in one of the conversion steps from 2 till 4. By the way, you need to check far more than these buttons. Pretty much has changed from 2 to 4, not for default behavior but for custom widgets, Java etc.
Hmm, strange that this option is set to true by default. Have you tried to do an import in a later Mendix version of 4? And how did you go to 4? From 2 to 3 and then to 4 or did you jump from 2 to 4?
Regards,
Ronald