I had this reply from Iain Robertson on an Adobe Forum. I've not tested this yet as I'm busy, busy, busy!
I think it is a “feature”, although one that flummoxed me to begin with. With the help of this forum I realised what you need to do is open one of your documents and open all your paragraph styles and use the new Export Tagging feature to map your paragraph style to an html tag. You can also add a class name. Do the same for your character styles. Then you have to synchronise the rest of the book with that one document as the source, so the new styles are used through all your documents. Then you have to create your own CSS file to apply style declarations to each tag plus any classes you created. This will mean your Indesign styles will get converted on output to consistent style names in the ePub and then styled by your CSS file. Make sure any class names you add in Export Tagging don't contain any spaces (use hyphens instead) and I think it is best to avoid capitals to be on the safe side.
That worked for me. It was a pain to begin with, compared to how I used to use CS5, but it seems sensible now! Haven't got time to go into more detail now but there is plenty info out there about the Export Tagging feature – make a test file and give it a whirl. I'm not the best person to describe how to make-up your CSS file – I'm making it up as I go along but there's loads of useful info out there about CSS – I particularly recommend w3schools.com (https://www.w3schools.com/css/c….._intro.asp).
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