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Sorry to reply to such an old topic, but to clarify ePubFixer does not just extract the opf and ncx and replace them it will recreate the ncx by looking at the opf and update the paths.
If the file that was referenced was removed or renamed it cannot find it and just puts an empty source has the file. So it is suggested to open the TOC editor and resave it, has it will remove any invalid path.
This might also be an old version that had a bug. But just to let people know that it was not just replacing the ncx, it recreates it.
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