For info the sequence at bay is

foo.set(bar); //@ContainedId
em.merge(foo);
em.flush();
em.clear();
commit();

We are trying to see if that sequence is common and makes sense in real life (i.e. aside from tests).

We could try and make that work but it would require to:

• detect that a flush happens (some kind of flag that would be cleared by a search flush)
• upon pre-clear, aggressively build the Document objects and keep them around
• upon commit, build the remaining Documents (potential second flush) and write the old and new documents

That's a fairly heavy work. We would prefer not to have to spend that energy here if the use case is uncommon.

Marc Schipperheyn can you describe in more detail the use case you ahve for a em.flush(); em.clear(); commit(); sequence?