Hello Jim!
I don't have either of the settings in my personal.ini, but will use the third option (replace_br_with_p: true) from now on. Hopefully that will stop the 'lost' paragraphs from happening.
Thank you!
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Update:
I added the setting replace_br_with_p: true and deleted the old ebook and downloaded it againg (just to be sure, because in addition I have problems with the replace_metadata in this story). Then I have uploaded the story onto my reader.
It has the exact same passages missing.
I don't know what's wrong. So, I am uploading the complete personal.ini and the ebook and hope that's something fixable. I appreciate any help, as always.