This might provide you with help concerning this issue. I format my ebooks using my word processor and then use it to generate a PDF for my ereader.
To ensure that the scene heading marker (such as "***" or "- - -") doesn't get end up at the bottom of a page, I make a paragraph style called "Interruption" and apply it to the markers. I then set the style to ensure that anything marked as with the Interruption style will not be separated from the next paragraph. If the marker falls at the bottom of a page, it will automatically be bumped to the next page so it stays with the next paragraph.
I hope that helps.
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