IIRC if you hit the Esc key during the game you can click on Options and there's a reset option in there somewhere that will undo whatever default responses you selected earlier in-game.
Then the next time one of those boxes pops up saying 'enemy ship sighted' or whatever and asks you how you want to respond to it, you can check the 'maintain current orders' box instead and set that as the default response. That way when that same situation happens again you can respond to it as you see fit without going through the 'what do you want to do' box at all.
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