The JES Service Registry (SR) deploys into Application Server 8.2 Enterprise Edition as part of the JES 5 release. The SR uses client certificate authentication to authenticate registered users. The SR has an option to generate a x509 certificate signed by the RegistryOperator certificate contained in the Application Server's truststore.
The problem is this client certificate authentication method depends on the location of the generated sun-web.xml file in the /generated/xml directory. When a deployed application is exploded and redeployed, the SR no longer know where to find the sun-web.xml file.
Modifying deployment descriptors after deployment is not recommended. If modifying a deployment descriptor after deployment is necessary, use the .reload functionality to force the application to reload. In the case of the Service Registry product, you will also need to modify the domain's web.xml file to include some login information. If you are having login issues, please double check to make sure their application is indeed reloaded by checking the server.log.