the ship will stop eventually, since its not accelerating anymore. all you can do is check your nav-menu and look for it, or fly into the direction it flew off. that are the only possibilities we have at the time. a system that allows better tracking of ships would be awesome.
another possibility would be using the 3d map, which you can open with p. but i dont know if your ship will sho up if you\'re not piloting it. i have to test this....