I write in Google Docs and the way I get it formatted correctly is ‘add space after paragraph’ which is the built-in space that ao3 has. Unfortunately I’m pretty sure the only way to fix it currently is just deleting the extra space in between manually after copy and pasting it in from notes or don’t add the extra spaces in your drafts going forward (but I am aware how difficult that is to look at/read while your working on it so I get it)

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