Calibre is about managing an eBook collection - it is not an eBook editing system. The merge facility in Calibre is about merging the information about two book entries in the Calibre database into a single entry - not merging the contents of the underlying eBooks.
I am afraid that what you want to do has to be done outside Calibre. What would be an appropriate tool will depend on what format the books are in. If you mention the format you may get some appropriate suggestions.
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