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FWIW: I had a similar issue with PG book last night. I wanted a MOBI file and didn't want to mess with my own conversion from their HTML. PG's ePub was a mess so I downloaded the MOBI which had spaces between the paragraphs.
I did a MOBI>EPUB and edited in Sigil to fix several small issues and found the space between paragraphs to be created using a styled paragraph containing a NBSP. It was on 3 lines and Sigil's Search&Replace couldn't handle finding a match (failed to deal with the line ending??) and I wasn't up to creating a successful RegEx.
When I reconverted EPUB>MOBI with Calibre, its legacy "remove spaces between paragraphs" (Look & Feel tab) failed to work. I then tried the new one on the Heuristic Processing tab which did the trick. Apparently the two use somewhat different logic.
Calibre is like a Swiss Army knife. If one blade isn't the right tool another probably is.
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