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Those "sidecar" files (and a folder / directory) are related to "MyClippings.txt" file. And MyClippings.txt is a log file Kindle firmware creates and constantly appends content to anytime you create a bookmark, highlight or a note inside any of your books.
That txt file is what most of "import your Kindle notes" type of programs use / parse to get bookmarks, notes and highlights since none of those developers are bothered to write code that parses those files in book's ".sdr" folder and extract the highlighted text from the book files themselves.
Just ignore MyClippings.txt and related files because even if you delete them they will just be recreated the first time you use UI to add bookmark / highlights / notes.
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