An applet runs inside a web browser and your jnlp file is still on the web server. So you can't access it via file system - even if you have the permission, because it is simply not there. Two possibilities:
1.)
Access your jnlp file via http://yourwebserver.domain/webproject/webcontent/lib/myfile.jnlp
2.)
Add your jnlp file to your applet.jar and load it with: getClass().getClassLoader().getResourceAsStream("myfile.jnlp");