Waypoints are created and saved to the unit internal memory ...
Deleting a waypoint in the Waypoint Management Menu removes the chosen waypoint(s) from the unit internal memory ... (It does not remove the Waypoint from an inserted SD card that holds Waypoint data) ...
So you are, in fact, deleting the Waypoint from the unit internal memory, but when you insert the card - that card still has the Waypoint data on it - and is being imported right back to the unit internal memory ...
To actually remove waypoints from an SD card - you will need to import the Waypoint Data into Humminbird PC / delete the chosen waypoint(s) / Upload the edited data back to the SD card and choose "Replace" during the upload procedure ...
Or you can delete the waypoint(s) in the Waypoint Management Menu of the unit and export the edited Waypoint data to a blank SD card ...
Rickie