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It's not a case of broken links... The search bug manifests when the toc does not have an entry for the file that the search is trying to navigate to.
Rebuilding the toc by "Files" will 'fix' it. Rebuilding the toc by other means, (such as importing an inline toc or Amazon Mobi style toc,) might not, depending on how complete the imported toc is.
This is most certainly a bug in Kobo firmware. There is no requirement for epub tocs to include every internal file. But there are many places, in Kepub reader and now the Epub reader, where Kobo devs mistakenly use the TOC as a substitute for the 'spine'. By spine, I'm refering to the section on the epub contends.opf file that lists all internal files and they order they are supposed to go. To avoid the known kobo quirks, (search in epubs, whole book page numbering and progress in kepub,) the ncx toc has to list the same contents as the spine.
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