To debug applications that contain programs in different languages, you need to debug the native COBOL and the non-COBOL code separately.
In Enterprise Developer for Eclipse, you can debug mixed native COBOL and Java using all COBOL target types.
You can debug native COBOL and C at the same time provided that the COBOL code has been compiled to .int code. In the COBOL Application debug configuration, you must uncheck the following option on the General tab and in the Debug Options section: Allow debugging of all COBOL target types (and disable mixed language debugging).