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@meme - no there is definitely a problem in there. In fact possibly two issues.
Open the Single file.epub. In Book View, place the cursor on the line before "Heading 1c", and do a split.
Now if you click on "link one", you will find it works, and you think "hey, no problem". However note that (1) if you switch back to the Section0002.html file and try to click it again the link does not work a second time (nor does link two). And (2) if you switch to code view and look at the underlying html that they remain as href="#Link_One" without the file prefix which explains why it won't work for subsequent clicks.
So I'm not sure why it works for that first click, and it seems it isn't doing all the relinking completely as far as the hrefs are concerned.
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