An EPUB can contain a chapter without listing it in the visible contents. That distinction is useful for interludes, copyright notices, dividers, or other pages readers should encounter in sequence but do not need as menu destinations. The safest EPUB table of contents workflow therefore tracks two decisions for every chapter: whether the XHTML remains in the book and whether a navigation link is generated for it.
The fixed STUDIO-247 specimen makes the difference measurable. It contains six chapters. Chapters two and four were marked not to appear in the contents, while chapters one, three, five, and six remained selected. Export preserved the six chapters in a nine-item spine and produced four NAV links, four NCX points, zero image resources, zero missing targets, and valid=true. Reader-button behavior was not operated, so the package facts and the visual navigation experience stay separate.
Write the Six-Chapter Contents Plan Before Export
Start with a small matrix rather than toggling chapters from memory. The rows are chapters one through six. The expected contents flags are true, false, true, false, true, true. Add a second column that says all six chapters remain included as reading content. This makes the intent reviewable before any package exists.
The important question is not simply “how many links?” It is “which four chapters should receive links, and which two should remain body-only?” Record each chapter’s opening marker and source path. A later reviewer can then distinguish chapter two from a similarly named divider and can detect an accidental reorder.
Change Only the Contents Flags for Chapters Two and Four
Apply the omission to chapters two and four without removing their source files from the selected book. Save the resulting workspace state and reread the six flags. If the application reports a successful setting change but the saved selection still shows all six as listed, stop before export. A returned success value and persisted state answer different questions.
This is also where destructive shortcuts cause trouble. Deleting the files or clearing their book selection can make the menu count appear correct while removing content. The desired state is narrower: six content chapters, four navigation entries. Keep that sentence beside the operation so another operator knows what must not change.
Read the Spine Separately from NAV and NCX
The generated EPUB has a nine-item spine. In this fixture, that count covers the six chapter documents plus the generated structural pages. Its navigation document has four list items, and toc.ncx has four navPoint elements. The four selected chapter labels and destinations correspond to chapters one, three, five, and six.
Do not combine these counts into one “EPUB is fine” checkbox. The spine answers what participates in reading order. NAV is the EPUB navigation document, while NCX provides a compatibility route for older systems. Matching four-and-four is useful, but the six chapter XHTML entries must also be present. Package inspection records zero images and zero missing references for this specimen.
Confirm the Omitted Chapters Were Not Deleted
Open the EPUB as a ZIP and locate all six chapter XHTML files. Resolve the spine item references in order and compare their headings with the source plan. Chapters two and four must still have content entries even though no corresponding NAV or NCX row is expected. This is the central acceptance test, not a side effect.
A future reader test can add another observation: advance from chapter one into chapter two, and from chapter three into chapter four, then reopen the contents panel and confirm that only the four selected chapters appear. That visual and interactive route was not measured in the retained run. The structural presence of chapters two and four does not prove how a particular reader’s next-page control behaves.
Recover a Missing Chapter Without Patching the EPUB
A clear failure is a package with four navigation links but only four chapter documents in the reading order. Preserve that EPUB and its digest. Return to the workspace, restore content inclusion for the missing chapter while leaving its contents flag off, and export under a new filename. Editing the packaged OPF directly may create a passing inspection once, but the next export will reproduce the source mistake.
Another failure is an old export in which all six contents links remain. Compare the artifact digest before diagnosing settings. Correct only the wrong flags, generate a new package, then repeat both the spine and navigation checks. A narrow repair can alter order or destinations, so previously passing rows are not exempt from the rerun.
Use Labels and Destinations, Not Counts Alone
Four links can still be wrong if one chapter is duplicated and another is missing. For each NAV row, record its displayed label, href, resolved XHTML file, and target heading. Repeat the destination comparison for the four NCX points. The accepted set is chapters one, three, five, and six with no duplicated destination.
This worksheet also catches a stale label after a chapter rename. A reachable file does not make the label accurate, and a correct label does not ensure the href reaches the intended chapter. Keeping both columns turns a link count into a route audit.
Hand Off a Bounded Four-Link Result
The final receipt names the six source chapters, their six contents flags, the EPUB digest, the nine spine items, four NAV entries, four NCX entries, zero images, zero missing references, and local valid=true. It explicitly records that chapters two and four remain packaged but are absent from both contents forms. A second operator should be able to reopen the same digest and reproduce those values without the original editing session.
Keep retailer acceptance, identical pagination, and reader-button behavior out of this receipt. They need named environments and their own observations. The local result proves that one six-chapter package implements the planned four-link contents set; it does not claim that every reading system presents or traverses it identically.
