With a little help from some very nice people over on the Adobe Forums, some of yesterday's problems are now (mostly) solved.
Yes, there are issues with importing Word files into InDesign; both packages have suffered from feature creep over the last couple of versions, so the integration of file types only gets harder and harder.
But what really solved the issue was the appliance of old-style scientific trial and error. Going through the processes that InDesign automates by hand, and working out which one of them was causing the error. As it turns out, ID isn't keen on long footnotes which split across three or four pages (you know what? I'm not keen on them, either!) and as soon as that was taken out, everything worked perfectly.
Once again, the principle of working through a process and breaking it down into the most basic steps you can find to figure out what's going wrong gives results. Excellent. Now I can get back to what I was supposed to be doing, and automating as much of the typesetting as I can.
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