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That all depends on what you are trying to do exactly. Both Sigil and Calibre allow regular expression based search and replace which can be used to automate the tasks. Both Sigil and Calibre allow plugins that can auto process any loaded epub. But creating a Sigil or Calibre plugin requires some knowledge of python and some knowledge of the plugin interface mechanism. Sigil's is perhaps easier to learn by example and is limited to the contents of the ebook, whereas Calibre's plugins have a more complicated interface but can do more.
That said, if you know some python or how to use regular expressions (or .bat files and have a tool you use) and your books are all epubs, you should be able to write a script to open (unzip) each epub in a folder, process it as desired, re zip up the revised epub, and repeat.
So it is hard to help without some idea of the changes needed in detail.
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