The bug can be solved if after you got scammed by the game and your pristine S class living ship got transformed into a garbage shuttle C-class, just exit the game and reload your save game point that got created after you left your own ship.
Problem should be solved.
Hope that Hello Games will fix this bug after the next years maybe?
Edit: Continuation of below topic:
Welcome to the forum @SledgeFox
Is this still an issue? If it is, we can move this to the new Waypoint topic.
Hello sheralmyst, thank you for asking!
Yes the bug still exists in 4.05. Hope this will help other players, thank you!
I have never been able to complete the Living Ship quest (don’t ask! 
)
But has anyone tried just calling in a junker ship to your location once you find the Living Ship? Instead of leaving to go to the freighter to change ships, that is… I’m assuming the game will let you do that at that point?