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When you THOUGHT Calibre conversion was broken.

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First try other ebooks or Wordprocessor documents freshly made on another computer.

Symptoms:
Using "Docx" there would be no page breaks in AZW3, ePub or mobi. Mobi headings would have outline numbering. Importing the docx back into Libre Office Writer would "create" up to 10 "converted page" styles. About 280 6" x 9" pages.
Using "ODT" you'd get page breaks in all formats except mobi. Epub and Mobi would have the strange outline numbering.

Well, examining the converted output in Calibre Editor revealed the <li (with the usual heading stuff)> and </li> around Chapter "headings". So next I examined the LibreOffice Writer style settings. Looked OK.
Four hours later I upgraded from 5.1 to 6.2.2 and found that the ePub creator built into Writer sort of works, but very basic. Calibre happily made that into AZW3 and Mobi files that worked.

However I was not happy. I'd spent days editing the 60,000 words. If the document was broken, so were the backups. Of course I could may go back to revision 15 or 16 instead of current 19.

Went to bed.

In the morning I thought RTF! It will just about save the basics, all the text! I saved the contents to clip board (as it's a pig) expecting to have to recreate the chapter bookmarks (anchors), Saved as RTF. Deleted the Default template and selected one I'd never used. Closed Writer. Opened Writer and read RTF. Amazingly the Contents/links/bookmarks intact.
Saved ODT and MS format DOCX.
Tried both in Calibre with ePub, AZW3 and Mobi. No evil Outlining Numbers on Chapters or paragraph dividers such as ~, § and * * *
About HALF the page breaks missing.

Clicked on each heading in Writer Navigator, hit Backspace till the Chapter Title became "body text" at end of previous paragraph. Between 1 and 6 presses! Ah! Hit Enter and Ctrl 1 to make it back to a "Heading 1" style.
Save both formats again (I only use DOCX for export, and the ODT for edits).
Now epub, AZW3 and Mobi all perfect from DOCX. Using ODT the body text spacing too tight and some images left justified instead of centred. But I'd learnt a while ago that the DOCX format is converted best. Pity about ODT.

Moral
So all working again, like February. So if the document gets internally confused, try saving as RTF, exit and re-import to your native working format.
I do increment the version before deleting a passage.
I do increment the version before editing in annotations exported from proof reading on the Kobo H2O.
I do increment before rewriting or global changes.
If the RTF trick hadn't worked, I'd have typed in all new headings in a fresh file and pasted the body of each chapter into a plain text editor and then copy & pasted the pure text after the new heading. Because I have backups and never actually lost the edited text. It was the invisible formatting somehow messed up.

Maybe originally transferring it from MS Word 2002 (XP Office) to LibreOffice via .doc about two and a half years ago. The previous proof was a bit flaky on the Kobo and I'd not looked at it on PW3 or ancient Kindle.

But the Grammar checker (better than nothing) vanished as did off line Help when I upgraded LibreOffice 5.1 to 6.2.2, probably 6.1 is a better choice. Anyway the usual Linux sites explained how to fix that.

How many times did I have to reboot Linux? Only once because I shut down the laptop when I go to bed. :)

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