I suppose the easier solution is to have three ships placed in the CS (dock A, dock B and mid-ocean) and a quest script to enable-disable them at the right times.
On the other extreme, visually moving the ships would be a solution several orders of magnitude more complex to develop.
The script for the easy one could, at a given time, say 6 AM, check the player distance from the ship at dock A and, if the distance is more than 20,000 units (~5 cells), disable the ship.
At 6 PM, if the player is not close to dock B, enable the ship there, simulating the arrival
If the player is closer and can see the ship, you delay the 'departure' until the player either leave the area (in which case you disable the ship) or board the ship and enter the cabin.
You also need three overlapping doors inside the cabin leading to the three ships. If the player is in the cabin, you enable the door leading to the ship in mid ocean during the period of the trip. After some time, as soon as the player enters the cabin, you enable the door leading to the ship in dock B and the ship itself.
The same approach can be used to the trip back, of course.