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The rule is very simple: Atlantis creates as many flow breaks in EPUB as hard page breaks in the source document.
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Two notes regarding this rule:
1. If your source document contains
chapters larger than 300 KB (when saved as XHTML), Atlantis automatically creates additional page breaks within such chapters in order to produce smaller XHTMLs.
2. If your source document contains footnotes and/or endnotes, Atlantis puts them into a separate HTML file. As a result, there is a page break before notes when viewed in eReaders.