[Quoth]

To enter proof annotations:

1. Open KATE/Notepad++ session for the project
2. Kobo Utilities to quickly read annotations only for the selected book. (in Calibre)
3. Copy & Paste into a new KATE/Notepad++ tab (added to session)
4. Save (annotate)_<title>_<version>.txt, in book directory use Regex to have annotations in format desired. Save.
5. Open book. SaveAs with updated version prefix if last version = annotation version.
6. Have annotations in left window (KATE or Notepad++ tabbed editor). Can select other tabs for cast, events, timeline.
7. Right window is Word or LO Writer.
8. Use ¬ to mark bits needing re-written or added, with comment, but otherwise only edit typos. Mark off note in Annotation window with *. The source txt of highlight is used in WP search.
9. Then when annotations all used up, remove it from session.
10. THEN do rewriting, but if any passage is to be deleted: Save, then Save As with version increment.

1. Check all anchors / TOC links still are correct
2. replace 2 space with 1 space till not found.
3. Then run regexs to find all other typos, leading spaces, trailing spaces etc.
4. Spelling and Grammar check.
5. Save As Docx if Writer (use ODT native), or use Docx native in Word.
6. Import to ePub2 conversion (Calibre / Sigil). Try NOT to edit, if MUST edit, only edit CSS.
7. Leave aside for a week or two and then proof/annotate on eReader again. H2O, Libra or Forma.

Save regularly. Esp at each step.
Create other eBook formats from epub2.
POD/Paper/PDF: Use a Save As copy of source and edit ONLY the styles. If for paper, remove all links.
Backup to elsewhere a couple of times a day, ALL changed files.
If you think you need fancier than KF8 or epub2, then maybe you need a PDF (many big colour images, or text book or fixed layout) or a custom app (multimedia).
Though most ebooks are read on phones and tablets, the point is that they are books that should reflow for 5" to 14" screens.