It only happens in two documents that have the same basic structure. One was based on the other, which probably explains why both have this “disease”! Exporting to IDML was the first thing I did when the problem occurred, but it did not solve the problem. I’m currently recreating one of the documents from scratch, and this new document seems to be “inoculated”! It will take quite a while to do as it’s a “spare time” sort of project, but the result will be worth it not to have this irritating warning pop up all the time.