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Calibre treats ZIP/RAR files containing a single ebook as though they were the unzipped version of the book. If you add some other dummy file to the ZIP/RAR so it contains files for more than a single book then it will leave it unchanged.
Just a bit of advice - you might be better off using RAR as your archive format. Calibre uses ZIP as a way of storing HTML based books (which typically consist of multiple files). It is therefore a good idea (although not mandated) to reserve ZIP for this type of book. I must admit I have no idea what would happen if you tried to add a HTML book (which Calibre puts into a ZIP) if you already have a ZIP containing books not in HTML format - my guess is it will replace them which will not be what you want.
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