ok, i need some help...
here's my workflow when doing clean-up of a number of books. regardless of how the book starts (solitary epub or epub+opf+cover), i always want the end result to be a single epub that contains the cover. one book, one file, all in.
so i load a book into calibre 2.13 and examine metadata & covers. i remove or clean up meta, blowing away ratings and other stuff so that i only keep the author, title, and series (if applicable). ALL other meta i deleted (supposedly). sometimes, the covers are ok but sometimes they're not, so i do a "download covers" and select an appropriate one from the options.
then, i do a "save to disk" with the following options: "save cover separately" and "separate opf" are UNchecked, but "update meta in saved copies" is checked.
if i then delete the book from the calibre library (but it stays in the saved directory) and i add that saved file back into calibre to verify - the cover is wrong. it's not the one i selected from the downloads. if i open that saved file in sigil, i can confirm that it's the wrong cover.
in some cases, tags that i blew away (isbn or ratings) are back.
i tried it with "update meta" UNchecked but that doesn't seem to make any difference.
i've just noticed this now, so i may have a few hundred epub files that have the wrong covers and extra tags, and i assume that if i redo my cleanup without changing how i do it, the files won't actually get cleaned up.