Since epubs are zip files, use a command line unzipper to unzip all to a folder.
Now you can use whatever S&R app or text editor you like that has a batch mode to edit the css and xhtml of all the files of interest at once. Even sed, perl, whatever.
Rezip-- I know that you need to zip without compressing the mimetype file, there are ways to do that, e.g.
epubpack.