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I have been working with very hierarchical data with FDS and EJB3.0 (hibernate on jboss4.0.5). I've avoided the direct mapping between flex and Hibernate because of scenarios like this. I don't like linking my persistence version/methodlogy directly to the front end. Instead I've used the JavaAssembler strategy that works directly with session EJBs. This has proven to work very well. Also you may be getting this error because your mappings are not correct. make sure your cascading properly. you will get this error because you're trying to insert an object that Hibernate has already inserted. hope this helps.
thanks for the reply it was very helpful. I came to pretty much the same conclusion and started on the path of a re-write of the hibernate assembler myself. As far as I can tell the Hibernate Assembler is a Java Assembler, so there didn't seem much difference to me between fixing that one and writing another one. Adobe ship the code.
Bit of a cheeky request, but I don't suppose you would be willing to share your assembler layer so I have a template against which to work? Biggest problem with this sort of activity is a lack of examples which makes it very slow going and largely trial and error.
If you would like to know more about our application I will provide contact details so we can discuss.
PS Jeff Vroom posted a reply saying that the Adobe Hibernate Assembler didn't work properly with hierarchical data (which I imagine is every real application in the world), personally I think Adobe should fix it or pull it.