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Sigil breaks existing TOCS when I open an ePub with it.
I've used it when it didn't break the TOC but most of the time it does so I'd always work on a copy if you use it. I don't any more I use notepad++ to edit the exported files and have only very rarely needed to work on an Indesign created TOC/NCX file. They have always been fine. Duplicate TOC entries might be due to one of the tick box selections in the export/content window.
I don't export to kindle with the kindle exporter from ID. I convert the ePub to mobi in Calibre for the Kindle store. That way I only have to edit the one package. Amazon has accepted them OK. I think they'd accept an ePub and convert it themselves for that matter.
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