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I did not follow through the migration path you list in the second edit, but your "out-of-date" comment in the first edit many well be the problem. So, two points:
1. When that 2009 SDDM white paper was published, the Data Modeler was not integrated into SQL Developer, it was standalone.
2. There is a dedicated forum for Data Modeler discussions: SQL Developer Data Modeler
Therefore, my recommendation would be either to:
1. Ask this question in the other forum.
2. Try an older, standalone version of Data Modeler. Trace back through the previous releases starting here: SQL Developer Data Modeler Downloads</title><meta name="Title" content="SQL Developer Data Model…
Thanks Gary for the informative reply and cross posting. What was the path you took for migration? was your base version was 1.3(designer 2k)?
...tracing earlier releases
My last exposure to Oracle Designer was quite long ago -- I was answering in the abstract. And the cross-posting upon reference to another forum became automatic some time after the Oracle forum upgrade in 2013.