There are 3 different situations that need to be addressed in existing projects.  In all cases, force regeneration of the build script by deleting nbproject/build-impl.xml and then loading the project into the IDE.

1) web apps with web service client:

   Open web.xml and for each service-ref entry (one for each JSR-109
   client in the project), change the mapping entry from

   <jaxrpc-mapping-file>WEB-INF/wsdl/[wsdl file
   name]-mapping.xml</jaxrpc-mapping-file>

   to

   <jaxrpc-mapping-file>WEB-INF/[wsdl file
   name]-mapping.xml</jaxrpc-mapping-file>


2)  web app or ejb jar (sub META-INF for WEB-INF if in ejbjar) with web service from either scratch or existing code:

   Open webservices.xml and for each webservice-description entry (one
   for each JSR-109 service in project), change the mapping entry from

   <jaxrpc-mapping-file>WEB-INF/wsdl/[service
   name]-mapping.xml</jaxrpc-mapping-file>

   to

   <jaxrpc-mapping-file>WEB-INF/[service
   name]-mapping.xml</jaxrpc-mapping-file>

3) web app or ejb jar (sub META-INF for WEB-INF if in ejbjar) with web service from wsdl (local or downloaded):

    Perform the steps in #2 above.

   In addition, go to the wsdl folder (Web Pages / WEB-INF / wsdl for
   web applications, or Configuration Files / wsdl for ejb jars).

   For each mapping file present here (should be one for each service
   that is created from a wsdl file), move the file up one folder to
   the WEB-INF or META-INF folder (Configurations Files)