I stopped using kepubs as soon as I discovered that the the driver was doing that. The epubs render the same as other ereaders and kindle and source in WP, the kepubs don't.
I do read what you say and pay attention.
Yes, if there is a TOC error, then the annotation doesn't work properly on the device. I saw that once on a draft that I'd not checked the headings/human contents page. So I always make sure that's correct.
Presumably Calibre has some internal recipe for generation of the file names. The only user control is the outer filename?
And no, I didn't look at the reports except at the start. I suspected it might be the same thing as before, but I'd not kept a copy, I'd have had to have looked for the previous post I made and compared line by line. I thought posting might be some help.
Obviously I was wrong.
I'll assume what ever this is will continue to be erratically appearing till there is a new Kobo Utilities that maybe has some reference to this.
Possible recreation if it's how I'm using Annotations:
Use 3 font faces: Chapter, body and divider/break. Ones that will work on Kobo, Kindle via Calibre embedding. All my embedded fonts working in epub (Kobo, Sony, Nook, phone apps), dual mobi on Kindle Keyboard and dual mobi and AZW3 on Kindle PW3.
Have a LibreOffice document with Chapter headings using a custom style, but level set to 1. Text Flow set to insert Page Before (but not with named style).
Put an anchor / bookmark in front of each heading.
Manually create text of contents and hyperlink to #ch1 etc. I do this by auto creation of a TOC without page numbers, cut and paste to a notepad, paste back. This means the text of all headings is in contents, but simply as plain text and then manually add the bookmarks/anchors as URLs (Select Line, Ctrl K, type #<anchor label> as URL, faster than using document url.
Only three styles body text needed: First Paragraph after chapters or breaks has no indent but a margin above. Break is centred Courier with bigger before margin and zero after, Default style has no margins above or below but a 1st line indent.
No other stuff needed.
Save as .odt
Save as MS Word .docx
Import to Calibre.
Convert to epub, but with setting to embed fonts used. Otherwise settings that don't change anything (I use "Tablet" to avoid image rescaling),
Convert epub rather than docx to dual mobi with all margins set to zero. View this and not the epub, as viewing the epub adds a bookmark that Daisy epub check complains about!
See that all TOC on dual mobi made from epub work. See that First Paragraph matches font size & internal line spacing of default paragraphs.
Transfer the epub from the docx to Kobo as epub
Do at least 40 annotations EVENTUALLY, but before done delete some, edit some, add book marks and delete them. Use some to jump to places in book. Take breaks and sleep Kobo.
Sometimes then the Annotations can be read by Kobo Utilities, sometimes not. They always can be read by the Annotations plugin.
Obviously I've no control over Calibre internal filename creation, though it's technically possible to edit those?
Only punctuation in outer file names is <single space> ’ , ( ) No accented letters, though I'd like á é í ó ú some things stupidly break with those as file names.
Every text has in the body and sometime chapters some combination of á é í ó ú also capitalised. That doesn't seem to be a problem for body. I've not checked if it's a problem for the TOC or headings/Chapters.
The Anchors/bookmarks are all each one string, no space or accents or punctuation, stuff like ch1 ch23 epilogue, not the actual chapter visible text. So the URLs in the contents page are simple, just those with # prefix, as you'd expect.