[Quoth]

I have no idea why sometimes it seems fine.


1) The Annotations plugin fetches the annotations the Kobo Utilies don't. So though they are different code the Annotations "copes silently" with what ever is the problem. This might be a clue. What extra thing or assumption is one or the other doing?
2) All the books are epubs. Not kepubs. I checked driver settings and on the Kobo info for book.
3) All the books pass the Daisy group epub check
4) All the books are produced using the same LibreOffice template, identical styles, workflow etc. Though the SF & F titles differ slightly, there is no correlation between failing imports and that.
5) There are no soft spaces. All spaces are ordinary and only single. No paragraph starts or ends with a space. There are no empty paragraphs. Checked with regex.
6) The sections at the start with URLS and at the end with images are identical. Only the body text and TOC differ. The main body and human readable contents page and the copyright page have no images. The failing & working "books" have exactly the same images and fonts.
7) TOC checked on every book before transfer to Kobo.
8) There are ONLY notes. No highlights or bookmarks.
9) No obvious difference between working and failing annotations imports.
10) The actual system Contents menu items match the human readable contents page that is always just before Chapter 1
11) Some books start the chapter title with Chapter (Fantasy) and others with just a number (SF titles). Makes no difference.
12) Logically it's SOMETHING in some books OR the way Kobo H20 original stores annotations. Could it be caused by adding an annotation and deleting it, or re-editing one, or adding bookmarks and deleting them. I do all of those. I could be how I'm using annotating and not the book itself?

The differences I see between Kobo Utilities and Annotations plugin fetching annotations:
a) Annotations has date & time on each note. Utilities has book progress instead, though it's called Chapter.
b) Utilities prefixes every chapter heading from the book with "Chapter nn: ", so you might see on each note: Chapter 0: Chapter 1: The Village
This is mysteriously zero based. The Annotations plug in simply has the actual text heading.

Also I didn't read the error as I'm not planing to fix it, so I didn't know I was posting something identical. They are not a personal criticism but simply a report.

I have no idea what goes on inside the plugins so all I can do is report when there is a problem. I do not keep a log of Kobo updates, Calibre Updates, Plug in Updates, Linux OS updates so when the error doesn't occur for ages, I might think something has changed and it's thus "fixed". This is in theory possible even if NO changes are made to the annotations fetching part of the Kobo Utilities as it's some unlikely event the software somewhere doesn't like. As the Annotations plugin works differently, I'd not assume its a bug in the Kobo Utilities, though it might be. The problem could be the Kobo, Calibre, the Plug in, Python or whatever.