The JSE deployment process rewrites the web.xml file and moves aside the original version. However, if I redeploy my ear file, the webservice stops working and throws a NoSuchMethodException from the ServiceEndpoint. It says it can't find the wsdl operation method. If I replace the web.xml file with the original, then redeploy the ear (allowing the deployment process to rewrite the web.xml again) everything works fine. I also noticed that if I don't rewrite the web.xml with the original, it creates multiple init-params for the Endpoint that are identical.
Regarding the multiple init-params, can you provide a simple war deployment that isolates the issue?