What kind of line breaks? You mean soft returns?
I bet he means entirely blank lines -- two returns in a row.
This has nothing to do with InDesign, it's just one of those things that's Not Supported by the ePub format, which is a poor man's HTML version.
(In real world HTML, the traditional way of forcing blank lines was to put a single non-breaking space on that blank line. Don't know if that works for ePub in general, or some ePub viewers. Just adjust the CSS, will you.)
Yes, I mean entirely empty lines. If that could be done with hard returns, I'd do that. But per Jongware, guess I'll have to work on the CSS. Thank you.