Answer:
Both "areas" of Bookmarks are linked, deleting from one will update the other. Neither are isolated personal storage areas for selected bookmarks of the user's choosing. You can't keep/delete one bookmark in one area (Bookmarks toolbar and/or hamburger icon > Bookmarks) without the action being correspondingly reflected in the other area.
New qustion:
Now I'm not joking here, but how does one go about trying to change this please?
