Usually, scenes where the camera tracks different objects are just set up as entirely different shots animated in different scene files. just like in real life different shots are indeed shot seperately.

Alternatively, if you want to have the camera smoothly transfer its tracking point from one object to another within one shot, you could use a null object (just make a cube or whatever and make it hidden) and parent/link the camera to the null object. Then you can have the null object follow your spaceship, and later move the null object to the new tracking location.

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