InDesign DOES remove all empty spaces...(which makes sense) If you ID file is correctly formatted using style sheets, then it will styled like this:
ChapterName
Body No Indent
body
body
body
bodySpaceabove
body
body
body
if you don't then after you make the epub. You need to edit the Template.CSS file (I use dreamweaver)
Copy and past the body style and simply add space above and rename it :
Code:
p.body {
font-family: "Minion Pro", serif;
line-height: 1.30em;
font-size: 0.96em;
margin-bottom: 0.00em;
margin-top: 0.00em;
text-indent: 0.00em;
margin-right: 0.00em;
margin-left: 0.00em;
text-align: justify;
font-weight: normal;
font-style: normal;
color: rgb(0,0,0);
p.bodyspaceabove {
font-family: "Minion Pro", serif;
line-height: 1.30em;
font-size: 0.96em;
margin-bottom: 0.00em;
margin-top: 1.5em;
text-indent: 0.00em;
margin-right: 0.00em;
margin-left: 0.00em;
text-align: justify;
font-weight: normal;
font-style: normal;
color: rgb(0,0,0);
Then go through you xhtml files and apply the relevant style.