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Sometimes (usually under heavy load) there are resource change events delivered to the WS model listener which deal with IType instances which fully qualified name is null. The null value of the qualified name later on leads to a NullPointerException in org.eclipse.jst.ws.jaxws.dom.runtime.persistence.sync.SeiSynchronizer / org.eclipse.jst.ws.jaxws.dom.runtime.persistence.sync.WsSynchronizer in their synchronize*() methods. This has been only observed in the automated tests environment and therefore I suspect a threading issue. Anyway, the model listener should disregard changes for such java elements since valid web service entities cannot be produced for such types.
Fixed in HEAD and release as v201101141643