I totally agree with you. I don't think it's a good idea to change the logic in a bugfix release so applying Yoann's fix for now is what I would have suggested.

Cool. So we agree to keep changes to a minimal. The one thing I don't like yet is that the whole if condition is very cryptic and implicit. AFAIU (see also comment on pull request) the condition occurs when I switch between one @IndexedEmbedded field/getter of a given entity to the next (provided there is one). Maybe instead of implicitly resetting we should make the code more explicit within initializeMemberLevelAnnotations. I think you might have meant this anyways when talking about "root entities" earlier. I give it a try whether this works and to see whether my theory is correct.

+1 for waiting for Marc's feedback. Once we have a solution we will have to apply it to at least 4.5 and the 5.0 dev branch. Not sure whether this single issue requires another 4.4 point release. That's open for discussion.