Open the XHTML generated in the ePUB file by InDesign. Are the "empty lines" there in any way (maybe an empty <P> or <DIV> tag)? If they are, you could post-process the ePUB to add something ( ) there.
If they aren't, there might be a way to run a macro/script that finds empty lines and adds a space or non-breaking space there. Then maybe when creating the ePUB these empty lines will not be lost.
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