Deleting a Waypoint...
 

Delete course plot waypoints in the game..

Manual says to use the 'Map/tools' button but there does not seem to be one as far as I can see. :hmmm:

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The fast and easy way is to use the eraser on the left side of screen.
Click it and then hold it over the waypoint you want gone and click again.
Becareful of where your line of travel goes after that though. It might put you right in the middle of an island.:yep:

Oh okay... Sure doesnt look like a 'tool button' though like the manual says

Cheers

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Geesh, been so long, might get the keys wrong, but I think shift del erases all waypoints at once, try clicking on your sub and try it.

The manual is pretty much useless. Like the red pencil on the left. Says you can use it to call in other forces but it doesn't work, least it doesn't for me.
There is better information here on this site than you will get out of the manual.

It can't even soak up bilge water. That's how useful it is!