[Dunati]

Frist, should probably put the ship on a solar escape trajectory, so that physically intercepting it would be more difficult with time, and likely require a technological leap to accomplish. It would also be nice to have the ship on a trajectory as far away from the plane of the ecliptic as you can, to minimize occlusion and time variation based on the earth's orbit.

Next, instead of pre-seeding the ship with keys, you have it generate them (using its RTG for both power and a source of entropy) and send them back to earth at a fixed rate, possibly with the size of the keys increasing over time.

On earth, when you want to encrypt a payload to be decrypted at a future date, you calculate how many round trips it would require, then encrypt the data with that many keys from the stream, interleaved with keys generated locally. As the time will unlikely be an exact round trip time (which is ever-increasing), each end can delay the decrypt and re-transmission for some proportion of the remaining time.