I found the problem - seemingly unrelated call to 'prepareGeometryChange' was to blame here. My widgets were changing size ( I didn't mention it, 'cause it seemed irrelevant at the time ). However I was calling the aforementioned method AFTER I made the change to the geometry, not before, as the manual instructs.
Apparently that method is very important in order to keep the scene's internal data in order, and due to my calling it incorrectly, it was leaving some invalid references to the deleted items.