If the eBook is already in InDesign, export that as an ePub and use Calibre's editor or Sigil to edit the ePub from there.
One thing you can do is show us one of these ePub from InDesign. But load the ePub in Calibre and install the Scramble eBook plugin and then attach the scrambled eBook so we can have a look at it and see what's going on.
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