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You can just delete the sdr folder for the book in a file browser like Total Commander if you're using Android. Or you just delete the metadata.epub(or pdf depending on the file).lua file in that folder.
In a test the bookmarks for the one book vanished after deleting the sdr folder.
The bookmarks also disappeared in the Bookmark Browser in KOReader.
But beware: the reading progress of that book disappears too in KOReader as does specific layout adjustments just for this book. Assuming you've finished this book you can just open it and go to the last page, so it's fully read again for KOReader.
The book still appears in the history though.
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