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You're screenshot didn't come through. What you're asking for is certainly doable, either directly in Calibre or via search and replace. That said, you're description doesn't have enough detail to provide you and specific help.
The screenshot would be a start, but enabling debug and presenting us some code snippets from the problem area would be most helpful. The best debug files would be the debug-raw from the input directory, and the html file in the structure directory.
Don't post the entire book here, just the snippets of the problem sections.
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