@monry,
I've no wish to cause further confusion
but ... rather than using conversion to fix the TOC have you considered using calibre's TOC Editor instead. It edits the TOC NCX not the in-book page(s) of hyperlinks.
If your original epub has a faulty TOC you can open it in the calibre TOC Editor where you can delete all existing TOC entries then choose the 'Generate TOC from files' option. This will guarantee that you get one entry per file. It may also mean some hand-editing of the TOC entry text if calibre has 'guessed wrong' what the label should be.
Once you know the epub TOC is perfect you can convert epub-to-kepub. You'll also need to make sure your conversion options don't interfere with the newly-perfected TOC, e.g. disable 'Force use of auto-generated TOC' and also check the settings on the Convert - Structure Detection page - particularly the 'Detect chapters at' option (I set mine to '/' when I want the TOC to be left alone)