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Ok, I figured this one out. If you have a document that you've made notes on and then copy a new document, with the same name, and over-write, then you will not be able to make notes on the second incarnation.
This is a problem for me of course because I do a lot of proofreading of my own texts, and then update them with the corrected version. Lesson learned. It is a minor inconvenience, because all I need to do, is to never over-write. First delete the old copy, and then copy the new one to it.
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