I think I know what's going on. When the message is shown, time slows down to 1 day/second, to give the player time to read and react. So it seems that distance and speed are stuck, but they're just changing very slowly. And while the ship is turning around, you can't use the engines (because that would steer the ship off course). I should probably make that clearer.
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Oh yes, it makes sense. While trying to take a screenshot of the bug, I also noticed that the ship was turning very slowly. There may be a 2-3 second animation that allows the ship to turn backwards beyond the player's control after the warning, but that could reduce the player's sense of freedom. Thanks a lot for your detailed explanations.