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I went with the same assumption that @Karellen did that you had a header in each file shown as <h4>Blah de blah<p></p>. I created an epub with 72 chapters which checkepub was very unhappy with. I then did a search for <p></p> and replaced with </h4> and the operation ran over all 72 chapters without issue.
The only way I could duplicate your issue was to select Current file instead of All text files.
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