If your SessionBeans are indeed talking to the same PersistenceContext then your code should be operating on the exact same Entities, no need to flush or refresh. It seems that your configuration may not be sharing the same PersistenceContext as you expect. Please make sure that you are not confusing Persistence Units for Persistence Contexts in your explanation. Are both Session Beans acting within the same transaction?
Perhaps you could provide details on your configuration including transaction states, call sequence and Session Bean transaction settings?
--Gordon
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