Originally Posted by Jaikon.Sorry to hear that the workaround did not work for you. You would possibly need to start a new save all together I am afraid.
I attempted to replicate this possible fix to no avail, sadly. Having cleared buildings around the ship/mouth of the river, the ship repeatedly sailed all the way south, exiting the map and returning bugged.
I have rolled back to various stages of this quest, but playing through to attempt completion results in a bugged quest every time.