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Not that I know of.
You have to "unpack" the mobi first, you can find the script (mobi2html) for that in the sticky mobi2mobi gui thread.
With a decent HTML editor, like notepad++ (Open Source & Free) you can clean up the code, and than use mobipocket creator to build the mobi file again (or the html2mobi command line tool).
With notepad++ you can search and replace several identical instances at once.
Example: if you look at the HTML and find all chapters start with <h2> tags, you can replace them with <mbp:pagebreak/><h2> and you get the break before the chapter...
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