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I've fixed several distinct issues with chapter splitting. There was one final problem with element ids and ToC generation that I only discovered and fixed yesterday, but that will go into the next release, which will be soon. Right now you have to make sure that all heading tags that aren't at the start of a flow have an id for the ToC to work properly, but that requirement will soon go away and Sigil will generate them automatically.
Split on SGF Chapter Markers should work exactly as expected in 0.4.0RC2, with no need to resort to workarounds or shuffle the files. The new chapters will now be placed in order immediately after the original chapter from which they were split and will be named [original file name]-0002, -0003, etc. This will work no matter where the original chapter is in the reading order.
Please test out 0.4.0RC2 and check that chapter splitting works properly in all cases. It was the main blocking issue that I wanted to resolve for the final release.
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