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Hmm, then manually regenerating it seems the best way forward, using Calibre or Sigil.
It's fairly straightforward in Sigil. Open the file, click the menu button and if you're lucky, the menu generates itself. If not, then you can stick <h> tags on the lines you want to be headers, then use the menu again.
In Calibre, I seem to remember there's a way to generate ToCs when format-shifting, or indeed converting epub to epub for that matter. The output options give you some control over it, and more so if you do a bit of research on how that particular dialog works.
I'd still recommend opening the file in Sigil, and running a validation check though. You never know - maybe it's something simple broken in the files which you can easily fix.
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