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You could wrap everything inside the body tag with a "div" or "section" tag if that is more appropriate. Then you use regular expression find and replace to replace the opening body tag with the opening body tag followed by an opening div tag, and then replace the closing body tag with a closing div followed by the closing body tag.
Also why on earth does any ebook have 1000 chapters. Something must be very broken or it is a fixed layout with 1000 pages of text.
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