Calibre probably isn't adding linebreaks it's just creating css for your paragraphs with large top and bottom margins, probably something like:
.calibrenn {
display: block;
margin-bottom: 1em;
margin-left: 0;
margin-right: 0;
margin-top: 1em
}
You could manually edit these to zero.
However, the easier option is to try running your conversion with Convert - Look&Feel - Remove spacing between paragraphs checked. See if you like the resulting epub better.
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