[KevinH]

You are including the cover.xhtml file in the OPF spine with linear="no" but the latest epubcheck requires that there be an existing link to any file included in the OPF spine.

The solution depends on epub version.

In epub2, you add the "cover" semantic to that file in the OPF guide thereby creating an external link to it.

In epub3, you add the "cover" semantic to that file in the NAV landmarks, thereby creating an external link to it from another xhtml file (in this case the Nav).

Alternatively, if you have a title page or html toc, you can simply create a normal hyperlink to that cover.xhtml and that should address that issue as well.

Aside: Why do you pay for something that free tools like epubcheck, Sigil, Calibre can provide? What advantage does Flightdeck actually provide? I am curious.