rule out possible PostgreSQL specifics

I think I pretty much ruled this out since I am running the production code on the same data with the exact same database and am simply changing the used Hibernate version between these runs (this why we see incremental id values on successive runs).

you could try to install a trigger on your DB to see which transaction deletes the row from the sub-table. A simple trigger that just raises an error should be enough to be able to identify the transaction.

Good idea - will see what I can do (I am not a DB expert and have to call on others for triggers ...).