The question really boils down to the dynamics of event horizons when black holes merge. It turns out that there are some great simulations that explore these dynamics. If one scrolls down to the bottom of this black-holes.org page one can see a video of the merging of two different sized black holes. One can review the underlying paper and see that the actual development of the simulation was very extensive.
The actual event horizons do move and oscillate, so the question is whether the spaceship itself has become some sort of physical element of the black hole after it has crossed the event horizon. Since it is argued in most cases that space craft can cross the event horizon in large black holes without witnessing any sort of significant effect, although the spacecraft's mass must be considered part of the black hole's mass after crossing the event horizon, it still has some freedom of movement.
We can see from the simulation that the geodesics that define the event horizon fluctuate when the holes merge. So if the geodesics fluctuate is it possible that the spacecraft would find itself on a geodesic that suddenly allows for an escape?
The answer should be no. The geodesics defining the horizon require trajectories with velocities greater than the speed of light. The spacecraft can not exceed the speed of light. So while the geodesic its on might distort during the merger of the black hole, it is the underlying space itself that is distorting, which is not going to impart some ability to defy local laws of physics to the space craft. As such, it will stay inside the blackhole horizon since its geodesic, while distorted, will still remain inside the horizon.