This might be a feature, but it's definitely a surprise.
I was just launching a sub with it's first and second destination set (via a waypoint) and that second destination appears to be locked now that the sub has launch. I didn't want to to cancel the launch in order to disable the waypoint because the timing is very, very tight for survivability. I figured, once it launches, I can cancel that waypoint as I see fit, but it appears to be set in stone.
Intended?
Cheers