Problem temporarily solved, but confusing: 10 minutes after posting the above, I changed a paragraph style definition and InDesign then decided to autoflow the text correctly. The change may have involved deciding the frame where a particular item starts, but either way, it could outflow. Why would InDesign then start autoflowing the text as a result?
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One of the options when defining a paragraph style is to set where does the paragraph starts, also you might get different results depending on how you selected the first frame when placing the long document.
Do not hesitate to add to this post with more details if this happens again.
I think this is somehow connected, although I don't know why it would be.
But I don't see why changing a paragraph style from starting in a new frame to 'anywhere' — after the text was placed — should have any effect on autoflow — it might jump to a new frame, but they're all threaded anyway. I'll see what happens when I place the next document.