What?
Select the bookmark.
Click Delete.
How much simpler can it be?
Wrong problem, wrong answer.
Try clicking on a known good bookmark *from the map*. Or select the bookmark (from the menu), and find that you can't navigate anywhere desirable from it due to the GalMap's plotting limitations. Or, just try plotting a route longer than sixty light years, from your bookmark in deep space.
The old school data collation and storage method. Unlimited storage, no batteries or charging, permanent, works offline: use a pen and paper. ¯\_(ツ)_/¯
Approved By Ben Ryder (tm).
Unfortunately, when I try OCR'ing the notes into the game, it comes out as an order for a Cambridge eel shop...