I have this problem with several cases in the latest two EAPs.
I have been successful to create a small problematic case:
com.sun.codemodel.JClass aclass = null;
aclass.binaryName(); //marked method as non existing
( ( com.sun.codemodel.JType ) aclass ).binaryName(); //marked method
as non existing
( ( com.sun.codemodel.JType ) aclass ).fullName();
Any ideas how I could resolve that?