Files exist in epub that are not listed in the manifest,
 

I am getting this error. Files exist in epub that are not listed in the manifest, they will be ignored.

cover.xhtml
Book.html
cover.jpeg
images/00005.jpg
TOC.xhtml
sgc-toc.css
Series.html
Dedication.html
dedication.html

Why are they ignored?

How can they be shown?

Basically, the epub is treated as if it is empty.

All your files must be listed in the manifest section of your opf file so that readers/devices know what’s in the ePub. You can enter them manually but Sigil will do it automatically if you use it’s “add files” function.

I would move the existing files to a folder on your desktop, so they are no longer in the ePub file, then add them using Sigil’s function (the + button)

Because the hrefs to them in the manifest section of the opf file are probably incorrect. Either that, or they are literally not included in the manifest section of the opf file.

By making the manifest hrefs to them correct (or adding them to the manifest if they're missing).

You wouldn't, by any chance, be using a slightly outdated version of the KindleImport plugin would you?