With MDM Workbench 9.0.x, you may find that web service deployment classes are not generated for data extensions. This causes runtime errors when invoking web services affected by data extensions, typically a class not found error referring to a class name with suffix _Ser, _Deser, or _Helper. Classes with these names should be generated when you run Prepare for Deployment on WSEJB projects. If these classes are not generated, the web service won't work.
To resolve this error, right-click on PartyWSEJB (you need to repeat this for each affected WSEJB project), select Properties. Select Project Facets. Check the facet: WebSphere EJB (Extended). Save changes, and run Prepare for Deployment on the WSEJB project.
I have added this information to the MDM Workbench FAQ. Thanks to Bark Bakker, for finding the workaround.
If you know of a good solution to a common problem, then please do add it to the MDM Workbench FAQ so that other users can benefit. And if you are having problems, please look at the MDM Workbench FAQ before posting to the MDM Workbench newsgroup, as you may find an answer there.