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Using JBDS 5 CR1 with SOA-tooling Beta 3, this error came back to life. I imported from two sources and created a simple view model which joined a table from each. Moved one source to a folder and the error came back.
An unexpected error occurred running the Create Workspace Preview VDB for "/CheckRefactoring/Books_Oracle.xmi" job.
An error creating the Preview VDB for model "/CheckRefactoring/Books_Oracle.xmi" occurred.
org.eclipse.core.internal.resources.ResourceException: Resource is out of sync with the file system: '/CheckRefactoring/Books_Oracle.xmi'.