In Windows you can rename the file extension from .epub to .zip, open the .zip file, delete the iTunesMetadata.plist file, the rename back to .epub. On a Mac I think there's a AppleScript somewhere on this forum that you can use to unzip and rezip the .epub after deleting the file. Also if I recall correctly Sigil removes unmanifested files from .epubs.
If I need to test a ebook in iTunes I always make a copy and open that because iTunes adds that file when you add an ebook.
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