Alda, I renamed a txt file to 'Font Book.app', and added it to a eupeb, saved, reloaded then right-cliked and removed it, and it did remove the file, so I can't suggest anything easy.
If you rename the epub and change it's extension, so it's a zip, open it in a prog such a 7zip, navigate to the OEBPS/Misc folder and delte the file, the re-save the zip, rename it back to epub, and you should be good to go.
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