I'm trying to add covers to epubs I've downloaded from Project Gutenberg. I'm following davidfor's suggestion and using Calibre's Polish books function. After I run that on the following book, when I open the folder where the book is in Calibre's library and double click on the epub file I get Sigil's warning "Files exist in epub that are not listed in the manifest, they will be ignored" and clicking on the details button lists nav.xhtml. If I unzip the epub and look at the content.opf file it does list the nav.xhtml file in the manifest section. If I save the epub and then open it again the error doesn't appear.
For Polish books, the options I have checked are Smarten punctuation, Update metadata in the book files, Update cover in the book files, and Upgrade book internals.
https://www.gutenberg.org/ebooks/16334 (the no images epub)
Any ideas why Sigil is giving that warning?