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Calibre will not be any help in the OCR side of this process in turning the images into text.
Calibre does have the facility of defining regex expressions for text (typically from headers and/or footers) that is to be omitted when converting a book. How well that would work in your case is likely to depend on the quality of the scanning/OCR process so that the text is predictable enough that a regex expression can be written to match the header/footer text.
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