I solved it. It was not NHibernate's fault. In my PostgreSQL database, I had a row level (before update) trigger on "Specimen" table which was returning NULL, so it was basically skipping the NHibernate second update (to associate the Specimen with the Case). That's why I was getting StaleStateException: The update affected 0 rows, and NHibernate expected it to affect 1 row.
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