To edit EPUB data safely, return to the source for each type of change and rebuild the package. Edit chapter text and headings in the manuscript, navigation inclusion in the chapter-order settings, the cover in its image setting, and author or publication details in the book metadata. In the controlled test for this article, one heading in chapter two changed from ESSAY377-02 to ESSAY377-02-改. Both the original and rebuilt packages returned valid=true in the local structural inspection.
That result did not make every expectation true. The sample had four essay chapters, but both nav and NCX contained five entries because the colophon source was also included in navigation. A successful export is therefore only part of the answer. The revised heading must appear, the cover and colophon must remain, and the navigation count must match the intended book.
Answer: edit the four sources, then rebuild the EPUB
An EPUB package contains several roles that should not be treated as one editable document. Manuscript files provide chapter content. Chapter order and inclusion settings determine reading order and navigation. A cover comes from its designated image. Metadata and colophon inputs provide publication details. Hand-editing generated files such as nav.xhtml or content.opf can create a result that is no longer reproducible from the source.
This test isolates one change: the chapter-two heading. The cover, author “朝凪遥,” publisher “Evidence Press,” publication date 2026-08-31, chapter list, and colophon source remain fixed. With only one controlled revision, a changed output can be attributed to that revision instead of an unrelated setting.
Sample and baseline: four chapters, one cover, one colophon
The dedicated copy contained chapters/01.md through 04.md, chapters/99-colophon.md, and images/cover.png. The series title was “四章随筆 STUDIO-377,” the file name was studio-377, the writing mode was horizontal, the language was Japanese, the volume number was 0, and the version was 1.0. The title-page position was supplied as 0 and the TOC-page position as 1.
Before editing, record the five source files in order, the cover path, the author, publisher, date, and the old chapter-two heading. Do not record “four TOC entries” as a fact until the generated nav and NCX have been inspected. This focus on rebuilding existing EPUB data differs from STUDIO-407, which covers the first local build, and STUDIO-481, which focuses on preserving repair destinations through a KDP manuscript revision.
Operation: change one heading and repeat the same build
The first pass set the series, volume, cover, selected files, title position, and TOC position. It then planned, exported, and inspected the EPUB. The source heading ESSAY377-02 was replaced with ESSAY377-02-改. The same cover and five-file list were applied again, followed by the same plan, export, and inspection sequence at a fixed time.
In the Rune Studio interface, the corresponding public workflow is the six-page EPUB Wizard: Series Information, Volume Selection, File Selection, Chapter Order, Metadata, and Review and Export. A chapter heading is repaired in its manuscript. Navigation inclusion is repaired in Chapter Order. The cover is repaired in Metadata. Author and publication values return to their series or volume inputs. This article does not assume a fictional “edit finished EPUB” screen.
Measured result: spine 9, nav 5, and NCX 5
The title-specific record has status=passed and command_count=16. Both builds were locally valid. The rebuilt spine contained nine resources: cover.xhtml, title.xhtml, nav.xhtml, p001.xhtml through p005.xhtml, and colophon.xhtml. It contained one image and zero missing images. Both nav and NCX were present.
The nav targets were p001.xhtml through p005.xhtml; the NCX targets were Text/p001.xhtml through Text/p005.xhtml. Each therefore had five entries. One controlled heading replacement was recorded, the first package was valid, and the EPUB SHA-256 changed after the edit. Both values in plan_chapter_counts were null, so this article does not infer a chapter count from the plan summary; it uses the inspected spine and navigation instead. These values show that the source revision reached a different rebuilt package.
They do not prove that a four-item TOC was achieved. If the intended navigation contains only the four essays, return to the navigation-inclusion setting for the colophon source and rebuild. Do not delete the fifth link from the generated nav by hand.
A separate common Stage 4 run verified the generic path with three chapters, horizontal writing mode, version 1.7, spine 7, one image, zero missing images, nav and NCX present, and valid=true in nine operations. That baseline does not replace the more specific 16-operation result above.
Limits: local validity is not retailer acceptance
The evidence covers the internal structure of EPUBs generated from a dedicated copy. valid=true does not mean KDP acceptance, successful retail listing, correct appearance in Kindle Previewer, or identical rendering in every reading system. No screenshots, device checks, or visual cover review were added in this text-only revision.
The five-entry result also does not establish a universal rule that every colophon must appear in navigation. It describes this sample: the colophon source was the fifth selected file and was not excluded from the TOC. Other books must be judged from their own source list and inclusion settings.
What Rune Studio contributes
Current documentation for Rune Studio on macOS describes a six-page EPUB Wizard that collects series information, volume details, source files, chapter order, navigation inclusion, cover, and publication data before generating EPUB 3. Its documented output includes XHTML content, title, navigation, colophon, cover, nav.xhtml, legacy-compatible NCX, and the metadata, manifest, and spine in content.opf. This is the documented Stage 3 product scope.
The navigation document, package document, and spine are roles defined by the EPUB 3.3 specification, not Rune-specific inventions. Rune Studio is one way to generate that structure. The Stage 4 findings above are limited to this controlled copy and operation record. The current Mac feature scope is also available on the Rune Studio product page.
Conclusion: reconcile the TOC count after every data edit
For an EPUB data edit, return each problem to its own source: chapter two for the heading, navigation inclusion for an extra TOC item, the cover setting for the cover, and the metadata or colophon source for publication details. In this sample, one heading revision produced a different EPUB while preserving spine 9, one image, zero missing images, five nav entries, five NCX entries, and local valid=true status.
Start by copying the manuscript and recording the exact source list and settings. If the rebuilt package contains five navigation entries when the intended TOC has four, return to the colophon’s inclusion setting. A reproducible source change plus an explicit repair destination is what prevents navigation, cover, or colophon data from being lost.
