I am not 100% certain of this answer but since no-one else has answered yet....
Let S be the frame in which the space ship is stationary and S' the frame in which the planet is stationary. The relative speed between the two frames is 0.98c so gamma is about 5.
From our seat in S we see the space surrounding the planet in S' to be shrunk by a factor of 5. So we observe the distance to the planet is 400e6/5 or 80 million meters. The information that the planet disappeared travels at 300 million meters per second so it takes 80/300 = 0.27 seconds to reach us.
We conclude that the planet disappeared 1.01-.27=0.74 seconds after the energy pulse. Provided the energy pulse travels faster than 80/0.74 = 108 million meters per second (about 0.36c) then there is no reason to doubt that is could have caused the destruction of the planet.