Working on this. However, short term workaround: "one shot delete". Instead of simply updating the Set and flushing, do something like:

Set oldSet = entity.getTheSet();
entity.setTheSet(new HashSet());
s.update(entity);
flush/commit
add all oldSet elements, new elements, etc. to entity.getTheSet()
flush/commit

That causes a "one-shot-delete" on the FK, rather than a one-by-one delete using the embeddable properties.