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The solution would be to create a standard workflow of book editing that you use to correct common problems and annoyances before you ever load the book onto your device and try to read it. If you make substantial edits to a book after the fact, it effectively becomes a different book. Kobo uses different rendering engines for EPUB vs KEPUB, so they're effectively separate environments. Even if you manually delete the old book and replace it with a new one, making certain kinds of changes will cause Kobo to treat it as a new book, even though it has the same name.
It is possible to export the annotations you've made in a book to a plain text file, and then you have a record of what you've highlighted in order to re-create the annotations by hand for the "new" book. You may wish to just do all your reference work on a separate device to avoid having to redo everything when you edit your books. You could also use KOReader to give yourself greater flexibility for book formatting to override badly formatted books without having to edit them.
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