Originally Posted by JSWolf
Here is how to do it so it comes out correctly...
1. Use Calibre to convert the PDF to ePub (do not use the delete blank lines option ever).
2. Use Sigil to edit the resulting ePub.
3. A/B compare the PDF to the ePub (every letter, every space, every punctuation, everything)
4. Edit the ePub to fix the errors.
5. Edit the ePub to fix the formatting.
6. Validate the ePub using FlightCrew.
7. Convert to AZW3 using Calibre.
To do this right takes a lot of work.
I came to this page via googling my issue which is the same as the OP. With all due respect, I would never want to do all that just to remove the annoying line spaces. I am not even sure that there are Windows alternatives for each program you have mentioned. I think if the author of Calibre was aware this as a high-priority bug, he would fix it. I have been using Calibre for a couple of years now (certainly not 30,000 posts long) and there are almost daily updates.
Bottom line – software should be able to do this. That's what PC's are for. There is a $.10 alternative.