I received your message and video, but I couldn’t reproduce the issue. Also, this is different procedure from the one you described above. You wrote:
I use ctrl+f2 to toggle off a bookmark then make some edits and save. When I reload the file, the bookmark is there. How do I permanently remove a bookmark?
But, the way you reload in the video is different, and do you want bookmarks turned on or off?
I have to ask again. Is “Save Cursor Position and Bookmarks” check box is set in the File page of the Customize dialog box?