Are you aware that when you use any of the kindle apps and you use the highlight/bookmark/notes that they will be uploaded to Amazon if they are Amazon books? If they are non-Amazon books then Calibre would be the best place to maintain those files. Although Calibre only has limited functionality for the files, you can use Calibre to fetch them from your kindle and then back them up on your hard drive or you can also use a plugboard template to upload the data into the metadata of the file, see here for instructions :
https://www.mobileread.com/forums/sho...d.php?t=100949
Sorry I do not know to point it to the exact page but it is the "Reading/read status custom column (Kindle) (pchrist7, w/ideas from beckywc):" one in the first post.
BTW: You asked a similar question regarding these files in four different places, which will make it harder for you to get some assistance.