[DiapDealer]

If you're not using any of calibre's automated "Beautify", "Fix html", or "Reorganize" features (and you've ensured that the ebook's metadata is not being updated before opening it in the editor), or you're not renaming files, then it (calibre) really shouldn't be changing anything you don't manually change yourself--certainly not in the opf file. It doesn't in my experience anyway. If you ARE doing/using any of those things with your epub3 book ... don't. It's not an epub3 "aware" editor (though it should handle html5 stuff OK).