In the following scenario only jboss-client.xml contains <service-ref> elements

<application-client version="5" xmlns="http://java.sun.com/xml/ns/javaee"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/application-client_5.xsd">

<display-name>TestEndpointService</display-name>

</application-client>

<jboss-client>
<jndi-name>jbossws-client</jndi-name>

<!--
@WebServiceRef(name = "Service1")
-->
<service-ref>
<service-ref-name>Service1</service-ref-name>
<service-impl-class>org.jboss.test.ws.jaxws.samples.webserviceref.TestEndpointService</service-impl-class>
<service-qname>

{http://org.jboss.ws/wsref}

TestEndpointService</service-qname>
<wsdl-override>META-INF/wsdl/TestEndpoint.wsdl</wsdl-override>
</service-ref>

<!--
@WebServiceRef(name = "Service2")
-->
<service-ref>
<service-ref-name>Service2</service-ref-name>
<config-name>Custom Client</config-name>
<config-file>META-INF/jbossws-client-config.xml</config-file>
<wsdl-override>META-INF/wsdl/TestEndpoint.wsdl</wsdl-override>
</service-ref>

<!--
@WebServiceRef(name = "Service3")
-->
<service-ref>
<service-ref-name>Service3</service-ref-name>
<service-impl-class>org.jboss.test.ws.jaxws.samples.webserviceref.TestEndpointService</service-impl-class>
<service-qname>

{http://org.jboss.ws/wsref}

TestEndpointService</service-qname>
<wsdl-override>META-INF/wsdl/TestEndpoint.wsdl</wsdl-override>
</service-ref>

<!--
@WebServiceRef(name = "Service4")
-->
<service-ref>
<service-ref-name>Service4</service-ref-name>
<port-component-ref>
<service-endpoint-interface>org.jboss.test.ws.jaxws.samples.webserviceref.TestEndpoint</service-endpoint-interface>
<config-name>Custom Client</config-name>
<config-file>META-INF/jbossws-client-config.xml</config-file>
</port-component-ref>
<wsdl-override>META-INF/wsdl/TestEndpoint.wsdl</wsdl-override>
</service-ref>

<!--
@WebServiceRef(name = "Port1", type = TestEndpoint.class)
-->
<service-ref>
<service-ref-name>Port1</service-ref-name>
<port-component-ref>
<port-qname>

{http://org.jboss.ws/wsref}

TestEndpointPort</port-qname>
<config-name>Custom Client</config-name>
<config-file>META-INF/jbossws-client-config.xml</config-file>
</port-component-ref>
<wsdl-override>META-INF/wsdl/TestEndpoint.wsdl</wsdl-override>
</service-ref>

<!--
@WebServiceRef(name = "Port2")
-->
<service-ref>
<service-ref-name>Port2</service-ref-name>
<port-component-ref>
<service-endpoint-interface>org.jboss.test.ws.jaxws.samples.webserviceref.TestEndpoint</service-endpoint-interface>
<config-name>Custom Client</config-name>
<config-file>META-INF/jbossws-client-config.xml</config-file>
</port-component-ref>
<wsdl-override>META-INF/wsdl/TestEndpoint.wsdl</wsdl-override>
</service-ref>

<!--
@WebServiceRef(name = "Port3")
-->
<service-ref>
<service-ref-name>Port3</service-ref-name>
<port-component-ref>
<service-endpoint-interface>org.jboss.test.ws.jaxws.samples.webserviceref.TestEndpoint</service-endpoint-interface>
<port-qname>

{http://org.jboss.ws/wsref}

TestEndpointPort</port-qname>
<stub-property>
<prop-name>javax.xml.ws.security.auth.username</prop-name>
<prop-value>kermit</prop-value>
</stub-property>
<stub-property>
<prop-name>javax.xml.ws.security.auth.password</prop-name>
<prop-value>thefrog</prop-value>
</stub-property>
</port-component-ref>
<wsdl-override>META-INF/wsdl/TestEndpoint.wsdl</wsdl-override>
</service-ref>

</jboss-client>

These are lost by

public static JBossServiceReferencesMetaData merge(ServiceReferencesMetaData override,
ServiceReferencesMetaData overriden,
String overridenFile, String overrideFile)

{ if (override == null && overriden == null) return null; JBossServiceReferencesMetaData merged = new JBossServiceReferencesMetaData(); JavaEEMetaDataUtil.merge(merged, overriden, override, "service-ref", overridenFile, overrideFile, false); return merged; }

because JavaEEMetaDataUtil.merge does nothing with merged if overridden is empty