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As near as I can tell the issue here is that sometimes you want an extra line but other times you don't. The problem is you are using a Paragraph mark as a line break whether or not you want an extra line. Different formats and programs interpret Paragraph marks differently. Calibre interprets it to mean that you want an extra line, as if to separate two paragraphs. It will do this *wherever* there is a Paragraph mark. You can, of course, tell Calibre to not add in extra line spaces. This will result in Calibre removing the extra line *wherever* there is a Paragraph Mark. It's a simple either/or logic statement. You can't ask it to just automatically know that sometimes it needs to disregard this logic statement without there being an identifying marker at those particular spots. What you need to do is edit the original RTF so that in the places where you do *not* want an extra line you need to replace it with a Manual Line Break. Is it a pain in the butt? Yes it is. Unfortunately it is the only way you are going to get it to convert reliably. Believe me I had to do it with nearly 700 files but I did it because I am extremely particular about how I want my files to appear.
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