For EPUB logical navigation, treat nav.xhtml as the primary EPUB 3 navigation and use NCX as a legacy-compatibility output that should point to the same chapters in the same order. The five-chapter sample in this article deliberately contains two headings named “Reunion.” Instead of assuming that labels are unique, the test compares five nav links with five NCX targets, from p001.xhtml through p005.xhtml.
Answer: Keep nav authoritative and reconcile NCX as compatibility output
Maintaining nav and NCX as two independently edited tables of contents invites drift in labels, order, and targets. A product-independent workflow keeps chapter order and stable targets in one source, uses the EPUB navigation document as the primary navigation, and checks the derived NCX for legacy compatibility.
Item count alone is not enough. Reconcile the visible label, sequence, and target for every entry. When “Reunion” occurs twice, its surrounding chapters and target files distinguish the entries. There is no need to rewrite a legitimate repeated heading merely to make every label unique.
Sample: Five chapters, two repeated labels, and five fixed markers
The article-specific sample used the title “旧リーダー互換 STUDIO-423,” author “Rune Verification,” publisher “Evidence Press,” horizontal Japanese layout, volume 0, version 1.0, and publication date 2026-08-31. It selected five manuscript files with title position 0 and TOC position 1. No cover image was supplied.
The source headings, in order, were 出航 (Departure), 再会 (Reunion), 岬 (Cape), 再会 (Reunion), and 帰港 (Homecoming). The sample retained five fixed markers even though one source label appeared twice. Its baseline was five chapters, two occurrences of the repeated heading, five fixed markers, five expected nav entries, and five expected NCX entries.
This arrangement is designed to expose three failures: merging repeated labels into one item, sending one repeated label to the wrong chapter, or changing the order in only one navigation format. Because the no-cover condition is intentional, zero images is not a failure in this sample.
Operation: Generate nav and NCX from the same chapter order
In a product-independent process, record the five-chapter order and one stable target for each chapter before generation. Afterward, compare each nav label and href with the corresponding NCX label and src. For the repeated labels, verify that positions 2 and 4 remain separate targets instead of relying on text matching alone.
For the Rune Studio run, work and version metadata were set and the five chapters were selected in order. The workflow reviewed the export plan, ran export and inspect, then read nav.xhtml, NCX, the five body XHTML files, and the package spine. It also checked that all five fixed markers remained present and that no resource was missing.
If the outputs disagree, do not patch only the generated NCX. When both formats have the same ordering error, return to the manuscript list. When only one target differs, return to the fixed target and generation settings. When two identical labels collapse into one, return to heading extraction and target mapping. Rebuild both navigation formats from the same source.
Measurement: Five entries in both formats with repeated headings intact
The article-specific Stage 4 record has status=passed and command_count=9. Local inspection returned valid=true, spine_count=8, image_count=0, missing_images=0, has_nav=true, and has_ncx=true. Both nav and NCX contained five entries.
The nav targets were p001.xhtml, p002.xhtml, p003.xhtml, p004.xhtml, and p005.xhtml. The NCX targets were Text/p001.xhtml, Text/p002.xhtml, Text/p003.xhtml, Text/p004.xhtml, and Text/p005.xhtml. Their path prefixes differ, but both sequences cover body files 1 through 5 in the same order.
The result also recorded duplicate_reunion_count=2 and fixed_marker_count=5. This supports the narrow finding that the build retained both repeated headings and five distinct targets while producing five entries in each format. The eight-resource spine represented title, nav, five body chapters, and colophon. The image count was zero because the run had no cover.
A separate common Stage 4 run used five chapters, horizontal layout, version 1.3, and a cover. In nine commands it produced spine=9, one image, no missing images, nav and NCX present, and valid=true. That shared-path result does not replace the article-specific version 1.0 sample with no cover and two repeated headings.
Limits: Legacy-reader presentation was not tested on hardware
Here, valid=true, nav 5, and NCX 5 describe a local structural inspection of an EPUB generated from a dedicated copy. The test did not cover the way a specific legacy reader presents NCX, Kindle Previewer conversion, KDP submission or review, retailer acceptance, or matching presentation across all reading systems.
Five fixed markers establish only that five targets remained in this test fixture. They do not prove that every reader displays repeated labels identically, or that NCX replaces the EPUB 3 navigation document as the primary source. For external verification, keep the local result as one gate and record each target reader separately.
Return according to the failure. If nav and NCX shift at the same position, return to the five-file chapter order. If only one format points elsewhere, return to target mapping and generation. If only one “Reunion” remains, check manuscript selections 2 and 4. If a target is missing, return to the body XHTML and package manifest. If NCX is absent, return to the generation log.
Rune Studio’s role: Include nav and legacy-compatible NCX in one build
The EPUB 3.3 specification defines the EPUB navigation document’s navigation role. NCX comes from an older navigation model, so it should not become a second independently maintained source of truth for an EPUB 3 publication. This distinction does not guarantee acceptance by a particular retailer.
Rune Studio’s documented Mac workflow can set chapter order and TOC inclusion in its EPUB Wizard and generate EPUB 3 content including nav.xhtml, legacy-compatible NCX, body XHTML, title, colophon, and content.opf. The Stage 4 result above is a local measurement of how one generated package mapped five targets with repeated headings. Current product information is available on the Rune Studio product page.
Conclusion: Reconcile repeated labels by order and target
Use nav as the primary EPUB 3 navigation and regenerate NCX from the same five-chapter source for legacy compatibility. In this sample, 出航, 再会, 岬, 再会, and 帰港 remained distinct, and both navigation formats pointed to body files 1 through 5 in order.
For a production manuscript, verify count, label order, and targets together, using stable targets to distinguish repeated headings. This article ends at nav-to-NCX reconciliation. It does not turn local success into evidence about KDP navigation generation or presentation on a particular legacy reader.
