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Start over, convert with calibre, BUT on conversion->structure detection, change the 'chapter mark' from pagebreak to none. On Epub-Output set split files to 4000
(Then the whole text will be in one file)
Load converted epub in Sigil, searching (code-view) for '<h\d', then move up a few lines, and insert a Sigil Chapter Marker where you want the split, and repeat process for rest of file. Then when done, Tools->'Split on SGF Chapter Markers'.
Job Done.
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