I’m using LibreOffice Writer 6.4.6.2. I have some blank lines in my endnotes, not after every endnote, just some. I haven’t found a way to delete these occasional blank lines. When I turn on formatting marks they don’t show a extra paragraph mark.
Click edit below your question and use the paper clip to upload a reduced sample file (remove all sensible data before).
Either they exist in the note when you entered it or you added some direct formatting to the note paragraph when editing it. To make sure, select the offending notes and Ctrl+M.