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Maybe you can use Regular expression
If you have the HTML files converted from PDF, ( All PDF must be converted into HTML firstly, then to ePub) you can use a Regular Expression tool to replace all Chapter names to proper HTML code.
Such as if your chapter HTML code has a structure as
<b>Chapter 12</b>
You can use "<b>(Chapter \d+)</b>" to grab them all, and replace them to
"<h2>$1</h2>"
No matter what, this is a work needs professional knowledge on Regular Expression.
And if your Chapter names were written in various HTML code, they only can be grabbed manually.
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