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Moving to the InDesign EPUB forum.
Regarding the footnotes numbering issue -
- You mention you use InDesign's book feature to combine the different chapters into a single EPUB export: For each of these individual documents, check the following: Type > Document Footnote Options. What is the start number set to for each of the documents? Are these all sequentially continuing from the last number of the previous document in the Book? It could be you've skipped a number there maybe?
- Alternatively by manually changing numbers you might have inadvertently "broken" something. You can't manually highlight the number in the footnote text at the bottom of the page, and then change the number, as that won't update the in-text footnote reference number. So your footnotes would be out.
- My recommendation in that case I'd recommend that you re-insert the footnotes, using using InDesign's Type > Insert Footnote prior to doing an EPUB export again.
Regarding splitting the document at certain locations:
- When you enable Split Document, what other setting have you got enabled?
- If you use Based on Paragraph Style Export Tag, then check the paragraph style Export Tagging settings in the Paragraph Style Options dialog box. is 'Split Document' option selected? AND in the different chapters and front matter, check which paragraph style is applied to the first line of text in each paragraph that needs to break. Each of these would need to have a paragraph style applied to it that has the 'Split Document' option enabled.