A quick update on this in case anyone else encounters the same issue, I have solved the problem by trashing any InDesign caches and preferences I could find in the System Library. I kept the old preferences so if I have time to investigate further I’ll test restoring them to see if I can find which file was causing the problem.
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I’ve narrowed it down to the InDesign Defaults file. I restored all the original (broken) preferences folder and then swapped out just the AppPrefs.xml for a known good file, and that didn't fix the problem, but when I replaced the InDesign Defaults file with a new good file it fixed the problem. I switched back and forth between the good and bad Defaults file and confirmed that it's where the problem comes from.
The problematic Defaults file is about 8.2 mb while the good replacement is about 2.6 mb. Unfortunately it's not a readable file (e.g. not xml) so looking inside it doesn't help, although perhaps someone at Adobe would be interested to have the file.
I'm still prodding it to see if I can narrow it down further.
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Okay, I’ve found what I suspect is the problem, or at least close to it. It seems to occur when Preferences > File handling > Links > Check Links Before Opening Document is off. In this case, any placed CC Library items are marked as "Pending" in the Links panel, regardless that the CC Libraries panel shows the library is loaded and there's no warning triangle in the Links panel.
However, this isn't the whole problem, because although I can reproduce the problem reliably when InDesign is launched with a new Defaults file, and can turn the effect on and off but adjusting just that preference, when I go back to using the original Defaults file I can turn the setting on and off and it doesn't fix the issue. So there's something else in the mix.
There's another thread with a similar issue and conclusion, so there’s a bug in there somewhere. Having got this far, and wasted more than eight hours trying to solve the problem (with no help at all from Adobe, despite the money I pay them) I'm not shelving this and can only hope that someone at Adobe picks it up and fixes it. I have my broken file if Adobe wants it.