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There is a "Join paragraphs" command in Atlantis. It can remove unwanted paragraph end marks (in OCR-ed documents, for example).
Just select a text fragment that should be converted into one paragraph, and press Ctrl+Shift+U.
If text fragments representing logical paragraphs, are separated with blank paragraphs (see attached "Join pars (before).rtf"), you can select entire document (press Ctrl+A), then execute the "Join paragraphs" command (press Ctrl+Shift+U). You would get something like the attached "Join pars (after).rtf".
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