There is a better way to fix this if that is what you need. There are two separate tools in the compile settings that we can use to first add visual space between paragraphs, and then with the second tool, use that space to convert it to an actual empty line for Markdown to recognise separate paragraphs.
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Go into
File/Compile...and double-click on the Format you are using, to edit its settings. If you are not using the “Basic MultiMarkdown” or Pandoc starter, or a custom one made from it, I’d recommend giving it a try first, to see how it is set up. -
In the Section Layouts pane, select the layouts that print text, and click the “Override text and notes formatting” option at the bottom for each one.
The “Basic MultiMarkdown/Pandoc” formats are already configured to add visual space between lines. If you’re working from your own that you made from scratch, you may need to add paragraph spacing to the formatting.
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Next click on the Transformations pane in the sidebar and tick the Convert to plain text checkbox. The setting that is provided is best, just “Paragraph Spacing”. If you used indents and include that you could end up making everything a code block.
The last thing to be aware of is that if you use styles while writing, you’ll want to go into the Styles pane and make sure that any you use also have paragraph spacing. (Hint: make the compile format designer window wider, if you can’t see the line & paragraph spacing control.)
I would not recommend using Replacements for this, because that will spread apart everything, and that may break some kind of Markdown that need two lines to be together: like tables and definition lists. And so by extension, if you do use those things, it will be a good idea to make styles for them—if only to protect them from having their paragraph spacing changed.