Wow, this has a really long post title.
Basically what I just figured out is how to delete the default domain that is created by the integrated Application Server (weblogic) by Jdeveloper.
Open Terminal.app
cd ~/.jdeveloper/
Here you’ll find various folders, go into the one that resembles systemjdevversion for example
cd system12.1.2.0.40.66.68
then delete folder DefaultDomain
rm -Rf DefaultDomain
After this just restart jdeveloper and you can create a default domain again.